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this.readInt32(t+this.readInt32(t))}__has_identifier(t){if(4!=t.length)throw new Error("FlatBuffers: file identifier must be length 4");for(let e=0;e<4;e++)if(t.charCodeAt(e)!=this.readInt8(this.position()+4+e))return!1;return!0}createLong(t,e){return Sn.create(t,e)}createScalarList(t,e){const i=[];for(let n=0;nthis.minalign&&(this.minalign=t);const i=1+~(this.bb.capacity()-this.space+e)&t-1;for(;this.space=0&&0==this.vtable[e];e--);const i=e+1;for(;e>=0;e--)this.addInt16(0!=this.vtable[e]?t-this.vtable[e]:0);this.addInt16(t-this.object_start);const n=2*(i+2);this.addInt16(n);let r=0;const s=this.space;t:for(e=0;e=0;e--)this.writeInt8(t.charCodeAt(e))}this.prep(this.minalign,4+n),this.addOffset(t),n&&this.addInt32(this.bb.capacity()-this.space),this.bb.setPosition(this.space)}finishSizePrefixed(t,e){this.finish(t,e,!0)}requiredField(t,e){const i=this.bb.capacity()-t,n=i-this.bb.readInt32(i);if(0==this.bb.readInt16(n+e))throw new Error("FlatBuffers: field "+e+" must be set")}startVector(t,e,i){this.notNested(),this.vector_num_elems=e,this.prep(4,t*e),this.prep(i,t*e)}endVector(){return this.writeInt32(this.vector_num_elems),this.offset()}createSharedString(t){if(!t)return 0;if(this.string_maps||(this.string_maps=new Map),this.string_maps.has(t))return this.string_maps.get(t);const e=this.createString(t);return this.string_maps.set(t,e),e}createString(t){if(!t)return 0;let e;if(t instanceof Uint8Array)e=t;else{e=[];let i=0;for(;i=56320?r:(r<<10)+t.charCodeAt(i++)+-56613888,n<128?e.push(n):(n<2048?e.push(n>>6&31|192):(n<65536?e.push(n>>12&15|224):e.push(n>>18&7|240,n>>12&63|128),e.push(n>>6&63|128)),e.push(63&n|128))}}this.addInt8(0),this.startVector(1,e.length,1),this.bb.setPosition(this.space-=e.length);for(let t=0,i=this.space,n=this.bb.bytes();t=0;i--)t.addOffset(e[i]);return t.endVector()}static startChildrenVector(t,e){t.startVector(4,e,4)}static addCustomMetadata(t,e){t.addFieldOffset(6,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static endField(t){return t.endObject()}}class On{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsSchema(t,e){return(e||new On).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsSchema(t,e){return t.setPosition(t.position()+4),(e||new On).__init(t.readInt32(t.position())+t.position(),t)}endianness(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):Tn.Little}fields(t,e){const i=this.bb.__offset(this.bb_pos,6);return i?(e||new Fn).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}fieldsLength(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.__vector_len(this.bb_pos+t):0}customMetadata(t,e){const i=this.bb.__offset(this.bb_pos,8);return i?(e||new Ln).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}customMetadataLength(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.__vector_len(this.bb_pos+t):0}features(t){const e=this.bb.__offset(this.bb_pos,10);return e?this.bb.readInt64(this.bb.__vector(this.bb_pos+e)+8*t):this.bb.createLong(0,0)}featuresLength(){const t=this.bb.__offset(this.bb_pos,10);return t?this.bb.__vector_len(this.bb_pos+t):0}static startSchema(t){t.startObject(4)}static addEndianness(t,e){t.addFieldInt16(0,e,Tn.Little)}static addFields(t,e){t.addFieldOffset(1,e,0)}static createFieldsVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startFieldsVector(t,e){t.startVector(4,e,4)}static addCustomMetadata(t,e){t.addFieldOffset(2,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static addFeatures(t,e){t.addFieldOffset(3,e,0)}static createFeaturesVector(t,e){t.startVector(8,e.length,8);for(let i=e.length-1;i>=0;i--)t.addInt64(e[i]);return t.endVector()}static startFeaturesVector(t,e){t.startVector(8,e,8)}static endSchema(t){return t.endObject()}static finishSchemaBuffer(t,e){t.finish(e)}static finishSizePrefixedSchemaBuffer(t,e){t.finish(e,void 0,!0)}static createSchema(t,e,i,n,r){return On.startSchema(t),On.addEndianness(t,e),On.addFields(t,i),On.addCustomMetadata(t,n),On.addFeatures(t,r),On.endSchema(t)}}class Dn{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFooter(t,e){return(e||new Dn).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFooter(t,e){return t.setPosition(t.position()+4),(e||new Dn).__init(t.readInt32(t.position())+t.position(),t)}version(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):An.V1}schema(t){const e=this.bb.__offset(this.bb_pos,6);return e?(t||new On).__init(this.bb.__indirect(this.bb_pos+e),this.bb):null}dictionaries(t,e){const i=this.bb.__offset(this.bb_pos,8);return i?(e||new vn).__init(this.bb.__vector(this.bb_pos+i)+24*t,this.bb):null}dictionariesLength(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.__vector_len(this.bb_pos+t):0}recordBatches(t,e){const i=this.bb.__offset(this.bb_pos,10);return i?(e||new vn).__init(this.bb.__vector(this.bb_pos+i)+24*t,this.bb):null}recordBatchesLength(){const t=this.bb.__offset(this.bb_pos,10);return t?this.bb.__vector_len(this.bb_pos+t):0}customMetadata(t,e){const i=this.bb.__offset(this.bb_pos,12);return i?(e||new Ln).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}customMetadataLength(){const t=this.bb.__offset(this.bb_pos,12);return t?this.bb.__vector_len(this.bb_pos+t):0}static startFooter(t){t.startObject(5)}static addVersion(t,e){t.addFieldInt16(0,e,An.V1)}static addSchema(t,e){t.addFieldOffset(1,e,0)}static addDictionaries(t,e){t.addFieldOffset(2,e,0)}static startDictionariesVector(t,e){t.startVector(24,e,8)}static addRecordBatches(t,e){t.addFieldOffset(3,e,0)}static startRecordBatchesVector(t,e){t.startVector(24,e,8)}static addCustomMetadata(t,e){t.addFieldOffset(4,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static endFooter(t){return t.endObject()}static finishFooterBuffer(t,e){t.finish(e)}static finishSizePrefixedFooterBuffer(t,e){t.finish(e,void 0,!0)}}var Pn=Sn,zn=Rn,Un=Mn;class Vn{constructor(t,i=e.V4,n,r){this.schema=t,this.version=i,n&&(this._recordBatches=n),r&&(this._dictionaryBatches=r)}static decode(t){t=new Un(Y(t));const e=Dn.getRootAsFooter(t),i=Gi.decode(e.schema());return new Hn(i,e)}static encode(t){const i=new zn,n=Gi.encode(i,t.schema);Dn.startRecordBatchesVector(i,t.numRecordBatches);for(const e of[...t.recordBatches()].slice().reverse())jn.encode(i,e);const r=i.endVector();Dn.startDictionariesVector(i,t.numDictionaries);for(const e of[...t.dictionaryBatches()].slice().reverse())jn.encode(i,e);const s=i.endVector();return Dn.startFooter(i),Dn.addSchema(i,n),Dn.addVersion(i,e.V4),Dn.addRecordBatches(i,r),Dn.addDictionaries(i,s),Dn.finishFooterBuffer(i,Dn.endFooter(i)),i.asUint8Array()}get numRecordBatches(){return this._recordBatches.length}get numDictionaries(){return this._dictionaryBatches.length}*recordBatches(){for(let t,e=-1,i=this.numRecordBatches;++e=0&&t=0&&t=0&&t=0&&tqn(function*(t){let e,i,n,r,s=!1,o=[],a=0;({cmd:n,size:r}=yield null);const l=(h=t,function*(t,e){const i=function*(t){yield t},n="string"==typeof e||ArrayBuffer.isView(e)||e instanceof ArrayBuffer||e instanceof $?i(e):S(e)?e:i(e);return yield*Q(function*(e){let i=null;do{i=e.next(yield G(t,i))}while(!i.done)}(n[Symbol.iterator]())),new t}(Uint8Array,h))[Symbol.iterator]();var h;try{do{if(({done:e,value:i}=Number.isNaN(r-a)?l.next():l.next(r-a)),!e&&i.byteLength>0&&(o.push(i),a+=i.byteLength),e||r<=a)do{({cmd:n,size:r}=yield"peek"===n?W(o,r)[0]:([i,o,a]=W(o,r),i))}while(rqn(function(t){return D(this,arguments,(function*(){let e,i,n,r,s=!1,o=[],a=0;({cmd:n,size:r}=yield yield O(null));const l=(h=t,X(Uint8Array,h))[Symbol.asyncIterator]();var h;try{do{if(({done:e,value:i}=Number.isNaN(r-a)?yield O(l.next()):yield O(l.next(r-a))),!e&&i.byteLength>0&&(o.push(i),a+=i.byteLength),e||r<=a)do{({cmd:n,size:r}=yield yield O("peek"===n?W(o,r)[0]:([i,o,a]=W(o,r),i)))}while(rqn(function(t){return D(this,arguments,(function*(){let e,i,n,r=!1,s=!1,o=[],a=0;({cmd:i,size:n}=yield yield O(null));const l=new Wn(t);try{do{if(({done:r,value:e}=Number.isNaN(n-a)?yield O(l.read()):yield O(l.read(n-a))),!r&&e.byteLength>0&&(o.push(Y(e)),a+=e.byteLength),r||n<=a)do{({cmd:i,size:n}=yield yield O("peek"===i?W(o,n)[0]:([e,o,a]=W(o,n),e)))}while(nqn(function(t){return D(this,arguments,(function*(){const e=[];let i,n,r,s="error",o=!1,a=null,l=0,h=[];if(({cmd:i,size:n}=yield yield O(null)),t.isTTY)return yield yield O(new Uint8Array(0)),yield O(null);try{e[0]=Gn(t,"end"),e[1]=Gn(t,"error");do{if(e[2]=Gn(t,"readable"),[s,a]=yield O(Promise.race(e.map((t=>t[2])))),"error"===s)break;if((o="end"===s)||(Number.isFinite(n-l)?(r=Y(t.read(n-l)),r.byteLength0&&(h.push(r),l+=r.byteLength)),o||n<=l)do{({cmd:i,size:n}=yield yield O("peek"===i?W(h,n)[0]:([r,h,l]=W(h,n),r)))}while(n{for(const[i,n]of e)t.off(i,n);try{const e=t.destroy;e&&e.call(t,i),i=void 0}catch(t){i=t||i}finally{null!=i?r(i):n()}}))}(e,"error"===s?a:null))}return yield O(null)}))}(t)),toDOMStream(t,e){throw new Error('"toDOMStream" not available in this environment')},toNodeStream(t,e){throw new Error('"toNodeStream" not available in this environment')}},qn=t=>(t.next(),t);class Wn{constructor(t){this.source=t,this.reader=null,this.reader=this.source.getReader(),this.reader.closed.catch((()=>{}))}get closed(){return this.reader?this.reader.closed.catch((()=>{})):Promise.resolve()}releaseLock(){this.reader&&this.reader.releaseLock(),this.reader=null}cancel(t){return F(this,void 0,void 0,(function*(){const{reader:e,source:i}=this;e&&(yield e.cancel(t).catch((()=>{}))),i&&i.locked&&this.releaseLock()}))}read(t){return F(this,void 0,void 0,(function*(){if(0===t)return{done:null==this.reader,value:new Uint8Array(0)};const e=yield this.reader.read();return!e.done&&(e.value=Y(e)),e}))}}const Gn=(t,e)=>{const i=t=>n([e,t]);let n;return[e,i,new Promise((r=>(n=r)&&t.once(e,i)))]},Zn=Object.freeze({done:!0,value:void 0});class Yn{constructor(t){this._json=t}get schema(){return this._json.schema}get batches(){return this._json.batches||[]}get dictionaries(){return this._json.dictionaries||[]}}class Qn{tee(){return this._getDOMStream().tee()}pipe(t,e){return this._getNodeStream().pipe(t,e)}pipeTo(t,e){return this._getDOMStream().pipeTo(t,e)}pipeThrough(t,e){return this._getDOMStream().pipeThrough(t,e)}_getDOMStream(){return this._DOMStream||(this._DOMStream=this.toDOMStream())}_getNodeStream(){return this._nodeStream||(this._nodeStream=this.toNodeStream())}}class Xn extends Qn{constructor(){super(),this._values=[],this.resolvers=[],this._closedPromise=new Promise((t=>this._closedPromiseResolve=t))}get closed(){return this._closedPromise}cancel(t){return F(this,void 0,void 0,(function*(){yield this.return(t)}))}write(t){this._ensureOpen()&&(this.resolvers.length<=0?this._values.push(t):this.resolvers.shift().resolve({done:!1,value:t}))}abort(t){this._closedPromiseResolve&&(this.resolvers.length<=0?this._error={error:t}:this.resolvers.shift().reject({done:!0,value:t}))}close(){if(this._closedPromiseResolve){const{resolvers:t}=this;for(;t.length>0;)t.shift().resolve(Zn);this._closedPromiseResolve(),this._closedPromiseResolve=void 0}}[Symbol.asyncIterator](){return this}toDOMStream(t){return $n.toDOMStream(this._closedPromiseResolve||this._error?this:this._values,t)}toNodeStream(t){return $n.toNodeStream(this._closedPromiseResolve||this._error?this:this._values,t)}throw(t){return F(this,void 0,void 0,(function*(){return yield this.abort(t),Zn}))}return(t){return F(this,void 0,void 0,(function*(){return yield this.close(),Zn}))}read(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"read")).value}))}peek(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"peek")).value}))}next(...t){return this._values.length>0?Promise.resolve({done:!1,value:this._values.shift()}):this._error?Promise.reject({done:!0,value:this._error.error}):this._closedPromiseResolve?new Promise(((t,e)=>{this.resolvers.push({resolve:t,reject:e})})):Promise.resolve(Zn)}_ensureOpen(){if(this._closedPromiseResolve)return!0;throw new Error("AsyncQueue is closed")}}class Kn extends Xn{write(t){if((t=Y(t)).byteLength>0)return super.write(t)}toString(t=!1){return t?V(this.toUint8Array(!0)):this.toUint8Array(!1).then(V)}toUint8Array(t=!1){return t?W(this._values)[0]:(()=>F(this,void 0,void 0,(function*(){var t,e;const i=[];let n=0;try{for(var r,s=z(this);!(r=yield s.next()).done;){const t=r.value;i.push(t),n+=t.byteLength}}catch(e){t={error:e}}finally{try{r&&!r.done&&(e=s.return)&&(yield e.call(s))}finally{if(t)throw t.error}}return W(i,n)[0]})))()}}class Jn{constructor(t){t&&(this.source=new er($n.fromIterable(t)))}[Symbol.iterator](){return this}next(t){return this.source.next(t)}throw(t){return this.source.throw(t)}return(t){return this.source.return(t)}peek(t){return this.source.peek(t)}read(t){return this.source.read(t)}}class tr{constructor(t){t instanceof tr?this.source=t.source:t instanceof Kn?this.source=new ir($n.fromAsyncIterable(t)):L(t)?this.source=new ir($n.fromNodeStream(t)):R(t)?this.source=new ir($n.fromDOMStream(t)):E(t)?this.source=new ir($n.fromDOMStream(t.body)):S(t)?this.source=new ir($n.fromIterable(t)):(k(t)||C(t))&&(this.source=new ir($n.fromAsyncIterable(t)))}[Symbol.asyncIterator](){return this}next(t){return this.source.next(t)}throw(t){return this.source.throw(t)}return(t){return this.source.return(t)}get closed(){return this.source.closed}cancel(t){return this.source.cancel(t)}peek(t){return this.source.peek(t)}read(t){return this.source.read(t)}}class er{constructor(t){this.source=t}cancel(t){this.return(t)}peek(t){return this.next(t,"peek").value}read(t){return this.next(t,"read").value}next(t,e="read"){return this.source.next({cmd:e,size:t})}throw(t){return Object.create(this.source.throw&&this.source.throw(t)||Zn)}return(t){return Object.create(this.source.return&&this.source.return(t)||Zn)}}class ir{constructor(t){this.source=t,this._closedPromise=new Promise((t=>this._closedPromiseResolve=t))}cancel(t){return F(this,void 0,void 0,(function*(){yield this.return(t)}))}get closed(){return this._closedPromise}read(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"read")).value}))}peek(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"peek")).value}))}next(t,e="read"){return F(this,void 0,void 0,(function*(){return yield this.source.next({cmd:e,size:t})}))}throw(t){return F(this,void 0,void 0,(function*(){const e=this.source.throw&&(yield this.source.throw(t))||Zn;return this._closedPromiseResolve&&this._closedPromiseResolve(),this._closedPromiseResolve=void 0,Object.create(e)}))}return(t){return F(this,void 0,void 0,(function*(){const e=this.source.return&&(yield this.source.return(t))||Zn;return this._closedPromiseResolve&&this._closedPromiseResolve(),this._closedPromiseResolve=void 0,Object.create(e)}))}}class nr extends Jn{constructor(t,e){super(),this.position=0,this.buffer=Y(t),this.size=void 0===e?this.buffer.byteLength:e}readInt32(t){const{buffer:e,byteOffset:i}=this.readAt(t,4);return new DataView(e,i).getInt32(0,!0)}seek(t){return this.position=Math.min(t,this.size),tF(this,void 0,void 0,(function*(){this.size=(yield t.stat()).size,delete this._pending})))()}readInt32(t){return F(this,void 0,void 0,(function*(){const{buffer:e,byteOffset:i}=yield this.readAt(t,4);return new DataView(e,i).getInt32(0,!0)}))}seek(t){return F(this,void 0,void 0,(function*(){return this._pending&&(yield this._pending),this.position=Math.min(t,this.size),t>>16,65535&this.buffer[1],this.buffer[0]>>>16,65535&this.buffer[0]]),i=new Uint32Array([t.buffer[1]>>>16,65535&t.buffer[1],t.buffer[0]>>>16,65535&t.buffer[0]]);let n=e[3]*i[3];this.buffer[0]=65535&n;let r=n>>>16;return n=e[2]*i[3],r+=n,n=e[3]*i[2]>>>0,r+=n,this.buffer[0]+=r<<16,this.buffer[1]=r>>>0>>16,this.buffer[1]+=e[1]*i[3]+e[2]*i[2]+e[3]*i[1],this.buffer[1]+=e[0]*i[3]+e[1]*i[2]+e[2]*i[1]+e[3]*i[0]<<16,this}_plus(t){const e=this.buffer[0]+t.buffer[0]>>>0;this.buffer[1]+=t.buffer[1],e>>0&&++this.buffer[1],this.buffer[0]=e}lessThan(t){return this.buffer[1]>>0,e[2]=this.buffer[2]+t.buffer[2]>>>0,e[1]=this.buffer[1]+t.buffer[1]>>>0,e[0]=this.buffer[0]+t.buffer[0]>>>0,e[0]>>0&&++e[1],e[1]>>0&&++e[2],e[2]>>0&&++e[3],this.buffer[3]=e[3],this.buffer[2]=e[2],this.buffer[1]=e[1],this.buffer[0]=e[0],this}hex(){return`${sr(this.buffer[3])} ${sr(this.buffer[2])} ${sr(this.buffer[1])} ${sr(this.buffer[0])}`}static multiply(t,e){return new cr(new Uint32Array(t.buffer)).times(e)}static add(t,e){return new cr(new Uint32Array(t.buffer)).plus(e)}static from(t,e=new Uint32Array(4)){return cr.fromString("string"==typeof t?t:t.toString(),e)}static fromNumber(t,e=new Uint32Array(4)){return cr.fromString(t.toString(),e)}static fromString(t,e=new Uint32Array(4)){const i=t.startsWith("-"),n=t.length,r=new cr(e);for(let e=i?1:0;e0&&this.readData(t,i)||new Uint8Array(0)}readOffsets(t,e){return this.readData(t,e)}readTypeIds(t,e){return this.readData(t,e)}readData(t,{length:e,offset:i}=this.nextBufferRange()){return this.bytes.subarray(i,i+e)}readDictionary(t){return this.dictionaries.get(t.id)}}class dr extends ur{constructor(t,e,i,n){super(new Uint8Array(0),e,i,n),this.sources=t}readNullBitmap(t,e,{offset:i}=this.nextBufferRange()){return e<=0?new Uint8Array(0):xi(this.sources[i])}readOffsets(t,{offset:e}=this.nextBufferRange()){return G(Uint8Array,G(Int32Array,this.sources[e]))}readTypeIds(t,{offset:e}=this.nextBufferRange()){return G(Uint8Array,G(t.ArrayType,this.sources[e]))}readData(t,{offset:e}=this.nextBufferRange()){const{sources:i}=this;return Et.isTimestamp(t)||(Et.isInt(t)||Et.isTime(t))&&64===t.bitWidth||Et.isDate(t)&&t.unit===s.MILLISECOND?G(Uint8Array,hr.convertArray(i[e])):Et.isDecimal(t)?G(Uint8Array,cr.convertArray(i[e])):Et.isBinary(t)||Et.isFixedSizeBinary(t)?function(t){const e=t.join(""),i=new Uint8Array(e.length/2);for(let t=0;t>1]=Number.parseInt(e.slice(t,t+2),16);return i}(i[e]):Et.isBool(t)?xi(i[e]):Et.isUtf8(t)?j(i[e].join("")):G(Uint8Array,G(t.ArrayType,i[e].map((t=>+t))))}}var fr,pr,gr,mr,br,yr,vr,wr;!function(t){t[t.BUFFER=0]="BUFFER"}(fr||(fr={})),function(t){t[t.LZ4_FRAME=0]="LZ4_FRAME",t[t.ZSTD=1]="ZSTD"}(pr||(pr={}));class _r{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsBodyCompression(t,e){return(e||new _r).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsBodyCompression(t,e){return t.setPosition(t.position()+4),(e||new _r).__init(t.readInt32(t.position())+t.position(),t)}codec(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt8(this.bb_pos+t):pr.LZ4_FRAME}method(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readInt8(this.bb_pos+t):fr.BUFFER}static startBodyCompression(t){t.startObject(2)}static addCodec(t,e){t.addFieldInt8(0,e,pr.LZ4_FRAME)}static addMethod(t,e){t.addFieldInt8(1,e,fr.BUFFER)}static endBodyCompression(t){return t.endObject()}static createBodyCompression(t,e,i){return _r.startBodyCompression(t),_r.addCodec(t,e),_r.addMethod(t,i),_r.endBodyCompression(t)}}class xr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}offset(){return this.bb.readInt64(this.bb_pos)}length(){return this.bb.readInt64(this.bb_pos+8)}static sizeOf(){return 16}static createBuffer(t,e,i){return t.prep(8,16),t.writeInt64(i),t.writeInt64(e),t.offset()}}class kr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}length(){return this.bb.readInt64(this.bb_pos)}nullCount(){return this.bb.readInt64(this.bb_pos+8)}static sizeOf(){return 16}static createFieldNode(t,e,i){return t.prep(8,16),t.writeInt64(i),t.writeInt64(e),t.offset()}}class Sr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsRecordBatch(t,e){return(e||new Sr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsRecordBatch(t,e){return t.setPosition(t.position()+4),(e||new Sr).__init(t.readInt32(t.position())+t.position(),t)}length(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt64(this.bb_pos+t):this.bb.createLong(0,0)}nodes(t,e){const i=this.bb.__offset(this.bb_pos,6);return i?(e||new kr).__init(this.bb.__vector(this.bb_pos+i)+16*t,this.bb):null}nodesLength(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.__vector_len(this.bb_pos+t):0}buffers(t,e){const i=this.bb.__offset(this.bb_pos,8);return i?(e||new xr).__init(this.bb.__vector(this.bb_pos+i)+16*t,this.bb):null}buffersLength(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.__vector_len(this.bb_pos+t):0}compression(t){const e=this.bb.__offset(this.bb_pos,10);return e?(t||new _r).__init(this.bb.__indirect(this.bb_pos+e),this.bb):null}static startRecordBatch(t){t.startObject(4)}static addLength(t,e){t.addFieldInt64(0,e,t.createLong(0,0))}static addNodes(t,e){t.addFieldOffset(1,e,0)}static startNodesVector(t,e){t.startVector(16,e,8)}static addBuffers(t,e){t.addFieldOffset(2,e,0)}static startBuffersVector(t,e){t.startVector(16,e,8)}static addCompression(t,e){t.addFieldOffset(3,e,0)}static endRecordBatch(t){return t.endObject()}}class Cr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsDictionaryBatch(t,e){return(e||new Cr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsDictionaryBatch(t,e){return t.setPosition(t.position()+4),(e||new Cr).__init(t.readInt32(t.position())+t.position(),t)}id(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt64(this.bb_pos+t):this.bb.createLong(0,0)}data(t){const e=this.bb.__offset(this.bb_pos,6);return e?(t||new Sr).__init(this.bb.__indirect(this.bb_pos+e),this.bb):null}isDelta(){const t=this.bb.__offset(this.bb_pos,8);return!!t&&!!this.bb.readInt8(this.bb_pos+t)}static startDictionaryBatch(t){t.startObject(3)}static addId(t,e){t.addFieldInt64(0,e,t.createLong(0,0))}static addData(t,e){t.addFieldOffset(1,e,0)}static addIsDelta(t,e){t.addFieldInt8(2,+e,0)}static endDictionaryBatch(t){return t.endObject()}}!function(t){t[t.HALF=0]="HALF",t[t.SINGLE=1]="SINGLE",t[t.DOUBLE=2]="DOUBLE"}(gr||(gr={}));class Ar{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFloatingPoint(t,e){return(e||new Ar).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFloatingPoint(t,e){return t.setPosition(t.position()+4),(e||new Ar).__init(t.readInt32(t.position())+t.position(),t)}precision(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):gr.HALF}static startFloatingPoint(t){t.startObject(1)}static addPrecision(t,e){t.addFieldInt16(0,e,gr.HALF)}static endFloatingPoint(t){return t.endObject()}static createFloatingPoint(t,e){return Ar.startFloatingPoint(t),Ar.addPrecision(t,e),Ar.endFloatingPoint(t)}}class Tr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsDecimal(t,e){return(e||new Tr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsDecimal(t,e){return t.setPosition(t.position()+4),(e||new Tr).__init(t.readInt32(t.position())+t.position(),t)}precision(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt32(this.bb_pos+t):0}scale(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readInt32(this.bb_pos+t):0}bitWidth(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.readInt32(this.bb_pos+t):128}static startDecimal(t){t.startObject(3)}static addPrecision(t,e){t.addFieldInt32(0,e,0)}static addScale(t,e){t.addFieldInt32(1,e,0)}static addBitWidth(t,e){t.addFieldInt32(2,e,128)}static endDecimal(t){return t.endObject()}static createDecimal(t,e,i,n){return Tr.startDecimal(t),Tr.addPrecision(t,e),Tr.addScale(t,i),Tr.addBitWidth(t,n),Tr.endDecimal(t)}}!function(t){t[t.DAY=0]="DAY",t[t.MILLISECOND=1]="MILLISECOND"}(mr||(mr={}));class Ir{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsDate(t,e){return(e||new Ir).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsDate(t,e){return t.setPosition(t.position()+4),(e||new Ir).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):mr.MILLISECOND}static startDate(t){t.startObject(1)}static addUnit(t,e){t.addFieldInt16(0,e,mr.MILLISECOND)}static endDate(t){return t.endObject()}static createDate(t,e){return Ir.startDate(t),Ir.addUnit(t,e),Ir.endDate(t)}}!function(t){t[t.SECOND=0]="SECOND",t[t.MILLISECOND=1]="MILLISECOND",t[t.MICROSECOND=2]="MICROSECOND",t[t.NANOSECOND=3]="NANOSECOND"}(br||(br={}));class Er{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsTime(t,e){return(e||new Er).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsTime(t,e){return t.setPosition(t.position()+4),(e||new Er).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):br.MILLISECOND}bitWidth(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readInt32(this.bb_pos+t):32}static startTime(t){t.startObject(2)}static addUnit(t,e){t.addFieldInt16(0,e,br.MILLISECOND)}static addBitWidth(t,e){t.addFieldInt32(1,e,32)}static endTime(t){return t.endObject()}static createTime(t,e,i){return Er.startTime(t),Er.addUnit(t,e),Er.addBitWidth(t,i),Er.endTime(t)}}class Mr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsTimestamp(t,e){return(e||new Mr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsTimestamp(t,e){return t.setPosition(t.position()+4),(e||new Mr).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):br.SECOND}timezone(t){const e=this.bb.__offset(this.bb_pos,6);return e?this.bb.__string(this.bb_pos+e,t):null}static startTimestamp(t){t.startObject(2)}static addUnit(t,e){t.addFieldInt16(0,e,br.SECOND)}static addTimezone(t,e){t.addFieldOffset(1,e,0)}static endTimestamp(t){return t.endObject()}static createTimestamp(t,e,i){return Mr.startTimestamp(t),Mr.addUnit(t,e),Mr.addTimezone(t,i),Mr.endTimestamp(t)}}!function(t){t[t.YEAR_MONTH=0]="YEAR_MONTH",t[t.DAY_TIME=1]="DAY_TIME",t[t.MONTH_DAY_NANO=2]="MONTH_DAY_NANO"}(yr||(yr={}));class Rr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsInterval(t,e){return(e||new Rr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsInterval(t,e){return t.setPosition(t.position()+4),(e||new Rr).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):yr.YEAR_MONTH}static startInterval(t){t.startObject(1)}static addUnit(t,e){t.addFieldInt16(0,e,yr.YEAR_MONTH)}static endInterval(t){return t.endObject()}static createInterval(t,e){return Rr.startInterval(t),Rr.addUnit(t,e),Rr.endInterval(t)}}!function(t){t[t.Sparse=0]="Sparse",t[t.Dense=1]="Dense"}(vr||(vr={}));class Lr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsUnion(t,e){return(e||new Lr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsUnion(t,e){return t.setPosition(t.position()+4),(e||new Lr).__init(t.readInt32(t.position())+t.position(),t)}mode(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):vr.Sparse}typeIds(t){const e=this.bb.__offset(this.bb_pos,6);return e?this.bb.readInt32(this.bb.__vector(this.bb_pos+e)+4*t):0}typeIdsLength(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.__vector_len(this.bb_pos+t):0}typeIdsArray(){const t=this.bb.__offset(this.bb_pos,6);return t?new Int32Array(this.bb.bytes().buffer,this.bb.bytes().byteOffset+this.bb.__vector(this.bb_pos+t),this.bb.__vector_len(this.bb_pos+t)):null}static startUnion(t){t.startObject(2)}static addMode(t,e){t.addFieldInt16(0,e,vr.Sparse)}static addTypeIds(t,e){t.addFieldOffset(1,e,0)}static createTypeIdsVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addInt32(e[i]);return t.endVector()}static startTypeIdsVector(t,e){t.startVector(4,e,4)}static endUnion(t){return t.endObject()}static createUnion(t,e,i){return Lr.startUnion(t),Lr.addMode(t,e),Lr.addTypeIds(t,i),Lr.endUnion(t)}}class Br{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFixedSizeBinary(t,e){return(e||new Br).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFixedSizeBinary(t,e){return t.setPosition(t.position()+4),(e||new Br).__init(t.readInt32(t.position())+t.position(),t)}byteWidth(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt32(this.bb_pos+t):0}static startFixedSizeBinary(t){t.startObject(1)}static addByteWidth(t,e){t.addFieldInt32(0,e,0)}static endFixedSizeBinary(t){return t.endObject()}static createFixedSizeBinary(t,e){return Br.startFixedSizeBinary(t),Br.addByteWidth(t,e),Br.endFixedSizeBinary(t)}}class Nr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFixedSizeList(t,e){return(e||new Nr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFixedSizeList(t,e){return t.setPosition(t.position()+4),(e||new Nr).__init(t.readInt32(t.position())+t.position(),t)}listSize(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt32(this.bb_pos+t):0}static startFixedSizeList(t){t.startObject(1)}static addListSize(t,e){t.addFieldInt32(0,e,0)}static endFixedSizeList(t){return t.endObject()}static createFixedSizeList(t,e){return Nr.startFixedSizeList(t),Nr.addListSize(t,e),Nr.endFixedSizeList(t)}}class Fr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsMap(t,e){return(e||new Fr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsMap(t,e){return t.setPosition(t.position()+4),(e||new Fr).__init(t.readInt32(t.position())+t.position(),t)}keysSorted(){const t=this.bb.__offset(this.bb_pos,4);return!!t&&!!this.bb.readInt8(this.bb_pos+t)}static startMap(t){t.startObject(1)}static addKeysSorted(t,e){t.addFieldInt8(0,+e,0)}static endMap(t){return t.endObject()}static createMap(t,e){return Fr.startMap(t),Fr.addKeysSorted(t,e),Fr.endMap(t)}}!function(t){t[t.NONE=0]="NONE",t[t.Schema=1]="Schema",t[t.DictionaryBatch=2]="DictionaryBatch",t[t.RecordBatch=3]="RecordBatch",t[t.Tensor=4]="Tensor",t[t.SparseTensor=5]="SparseTensor"}(wr||(wr={}));class Or{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsMessage(t,e){return(e||new Or).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsMessage(t,e){return t.setPosition(t.position()+4),(e||new Or).__init(t.readInt32(t.position())+t.position(),t)}version(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):An.V1}headerType(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readUint8(this.bb_pos+t):wr.NONE}header(t){const e=this.bb.__offset(this.bb_pos,8);return e?this.bb.__union(t,this.bb_pos+e):null}bodyLength(){const t=this.bb.__offset(this.bb_pos,10);return t?this.bb.readInt64(this.bb_pos+t):this.bb.createLong(0,0)}customMetadata(t,e){const i=this.bb.__offset(this.bb_pos,12);return i?(e||new Ln).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}customMetadataLength(){const t=this.bb.__offset(this.bb_pos,12);return t?this.bb.__vector_len(this.bb_pos+t):0}static startMessage(t){t.startObject(5)}static addVersion(t,e){t.addFieldInt16(0,e,An.V1)}static addHeaderType(t,e){t.addFieldInt8(1,e,wr.NONE)}static addHeader(t,e){t.addFieldOffset(2,e,0)}static addBodyLength(t,e){t.addFieldInt64(3,e,t.createLong(0,0))}static addCustomMetadata(t,e){t.addFieldOffset(4,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static endMessage(t){return t.endObject()}static finishMessageBuffer(t,e){t.finish(e)}static finishSizePrefixedMessageBuffer(t,e){t.finish(e,void 0,!0)}static createMessage(t,e,i,n,r,s){return Or.startMessage(t),Or.addVersion(t,e),Or.addHeaderType(t,i),Or.addHeader(t,n),Or.addBodyLength(t,r),Or.addCustomMetadata(t,s),Or.endMessage(t)}}class Dr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsNull(t,e){return(e||new Dr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsNull(t,e){return t.setPosition(t.position()+4),(e||new Dr).__init(t.readInt32(t.position())+t.position(),t)}static startNull(t){t.startObject(0)}static endNull(t){return t.endObject()}static createNull(t){return Dr.startNull(t),Dr.endNull(t)}}class Pr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsBinary(t,e){return(e||new Pr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsBinary(t,e){return t.setPosition(t.position()+4),(e||new Pr).__init(t.readInt32(t.position())+t.position(),t)}static startBinary(t){t.startObject(0)}static endBinary(t){return t.endObject()}static createBinary(t){return Pr.startBinary(t),Pr.endBinary(t)}}class zr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsBool(t,e){return(e||new zr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsBool(t,e){return t.setPosition(t.position()+4),(e||new zr).__init(t.readInt32(t.position())+t.position(),t)}static startBool(t){t.startObject(0)}static endBool(t){return t.endObject()}static createBool(t){return zr.startBool(t),zr.endBool(t)}}class Ur{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsUtf8(t,e){return(e||new Ur).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsUtf8(t,e){return t.setPosition(t.position()+4),(e||new Ur).__init(t.readInt32(t.position())+t.position(),t)}static startUtf8(t){t.startObject(0)}static endUtf8(t){return t.endObject()}static createUtf8(t){return Ur.startUtf8(t),Ur.endUtf8(t)}}class Vr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsList(t,e){return(e||new Vr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsList(t,e){return t.setPosition(t.position()+4),(e||new Vr).__init(t.readInt32(t.position())+t.position(),t)}static startList(t){t.startObject(0)}static endList(t){return t.endObject()}static createList(t){return Vr.startList(t),Vr.endList(t)}}class Hr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsStruct_(t,e){return(e||new Hr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsStruct_(t,e){return t.setPosition(t.position()+4),(e||new Hr).__init(t.readInt32(t.position())+t.position(),t)}static startStruct_(t){t.startObject(0)}static endStruct_(t){return t.endObject()}static createStruct_(t){return Hr.startStruct_(t),Hr.endStruct_(t)}}var jr=Sn;const $r=new class extends Kt{visit(t,e){return null==t||null==e?void 0:super.visit(t,e)}visitNull(t,e){return Dr.startNull(e),Dr.endNull(e)}visitInt(t,e){return Bn.startInt(e),Bn.addBitWidth(e,t.bitWidth),Bn.addIsSigned(e,t.isSigned),Bn.endInt(e)}visitFloat(t,e){return Ar.startFloatingPoint(e),Ar.addPrecision(e,t.precision),Ar.endFloatingPoint(e)}visitBinary(t,e){return Pr.startBinary(e),Pr.endBinary(e)}visitBool(t,e){return zr.startBool(e),zr.endBool(e)}visitUtf8(t,e){return Ur.startUtf8(e),Ur.endUtf8(e)}visitDecimal(t,e){return Tr.startDecimal(e),Tr.addScale(e,t.scale),Tr.addPrecision(e,t.precision),Tr.addBitWidth(e,t.bitWidth),Tr.endDecimal(e)}visitDate(t,e){return Ir.startDate(e),Ir.addUnit(e,t.unit),Ir.endDate(e)}visitTime(t,e){return Er.startTime(e),Er.addUnit(e,t.unit),Er.addBitWidth(e,t.bitWidth),Er.endTime(e)}visitTimestamp(t,e){const i=t.timezone&&e.createString(t.timezone)||void 0;return Mr.startTimestamp(e),Mr.addUnit(e,t.unit),void 0!==i&&Mr.addTimezone(e,i),Mr.endTimestamp(e)}visitInterval(t,e){return Rr.startInterval(e),Rr.addUnit(e,t.unit),Rr.endInterval(e)}visitList(t,e){return Vr.startList(e),Vr.endList(e)}visitStruct(t,e){return Hr.startStruct_(e),Hr.endStruct_(e)}visitUnion(t,e){Lr.startTypeIdsVector(e,t.typeIds.length);const i=Lr.createTypeIdsVector(e,t.typeIds);return Lr.startUnion(e),Lr.addMode(e,t.mode),Lr.addTypeIds(e,i),Lr.endUnion(e)}visitDictionary(t,e){const i=this.visit(t.indices,e);return Nn.startDictionaryEncoding(e),Nn.addId(e,new jr(t.id,0)),Nn.addIsOrdered(e,t.isOrdered),void 0!==i&&Nn.addIndexType(e,i),Nn.endDictionaryEncoding(e)}visitFixedSizeBinary(t,e){return Br.startFixedSizeBinary(e),Br.addByteWidth(e,t.byteWidth),Br.endFixedSizeBinary(e)}visitFixedSizeList(t,e){return Nr.startFixedSizeList(e),Nr.addListSize(e,t.listSize),Nr.endFixedSizeList(e)}visitMap(t,e){return Fr.startMap(e),Fr.addKeysSorted(e,t.keysSorted),Fr.endMap(e)}};function qr(t){return new is(t.count,Gr(t.columns),Zr(t.columns))}function Wr(t,e){return(t.children||[]).filter(Boolean).map((t=>Zi.fromJSON(t,e)))}function Gr(t){return(t||[]).reduce(((t,e)=>{return[...t,new ss(e.count,(i=e.VALIDITY,(i||[]).reduce(((t,e)=>t+ +(0===e)),0))),...Gr(e.children)];var i}),[])}function Zr(t,e=[]){for(let i=-1,n=(t||[]).length;++in),this._bodyLength="number"==typeof t?t:t.low}static fromJSON(t,i){const n=new es(0,e.V4,i);return n._createHeader=function(t,e){return()=>{switch(e){case l.Schema:return Gi.fromJSON(t);case l.RecordBatch:return is.fromJSON(t);case l.DictionaryBatch:return ns.fromJSON(t)}throw new Error(`Unrecognized Message type: { name: ${l[e]}, type: ${e} }`)}}(t,i),n}static decode(t){t=new ts(Y(t));const e=Or.getRootAsMessage(t),i=e.bodyLength(),n=e.version(),r=e.headerType(),s=new es(i,n,r);return s._createHeader=function(t,e){return()=>{switch(e){case l.Schema:return Gi.decode(t.header(new On));case l.RecordBatch:return is.decode(t.header(new Sr),t.version());case l.DictionaryBatch:return ns.decode(t.header(new Cr),t.version())}throw new Error(`Unrecognized Message type: { name: ${l[e]}, type: ${e} }`)}}(e,r),s}static encode(t){const i=new Jr;let n=-1;return t.isSchema()?n=Gi.encode(i,t.header()):t.isRecordBatch()?n=is.encode(i,t.header()):t.isDictionaryBatch()&&(n=ns.encode(i,t.header())),Or.startMessage(i),Or.addVersion(i,e.V4),Or.addHeader(i,n),Or.addHeaderType(i,t.headerType),Or.addBodyLength(i,new Kr(t.bodyLength,0)),Or.finishMessageBuffer(i,Or.endMessage(i)),i.asUint8Array()}static from(t,i=0){if(t instanceof Gi)return new es(0,e.V4,l.Schema,t);if(t instanceof is)return new es(i,e.V4,l.RecordBatch,t);if(t instanceof ns)return new es(i,e.V4,l.DictionaryBatch,t);throw new Error(`Unrecognized Message header: ${t}`)}get type(){return this.headerType}get version(){return this._version}get headerType(){return this._headerType}get bodyLength(){return this._bodyLength}header(){return this._createHeader()}isSchema(){return this.headerType===l.Schema}isRecordBatch(){return this.headerType===l.RecordBatch}isDictionaryBatch(){return this.headerType===l.DictionaryBatch}}class is{constructor(t,e,i){this._nodes=e,this._buffers=i,this._length="number"==typeof t?t:t.low}get nodes(){return this._nodes}get length(){return this._length}get buffers(){return this._buffers}}class ns{constructor(t,e,i=!1){this._data=t,this._isDelta=i,this._id="number"==typeof e?e:e.low}get id(){return this._id}get data(){return this._data}get isDelta(){return this._isDelta}get length(){return this.data.length}get nodes(){return this.data.nodes}get buffers(){return this.data.buffers}}class rs{constructor(t,e){this.offset="number"==typeof t?t:t.low,this.length="number"==typeof e?e:e.low}}class ss{constructor(t,e){this.length="number"==typeof t?t:t.low,this.nullCount="number"==typeof e?e:e.low}}function os(t,e){const i=[];for(let n,r=-1,s=-1,o=t.childrenLength();++rZi.encode(t,e))),l=Fn.createChildrenVector(t,a),h=e.metadata&&e.metadata.size>0?Fn.createCustomMetadataVector(t,[...e.metadata].map((([e,i])=>{const n=t.createString(`${e}`),r=t.createString(`${i}`);return Ln.startKeyValue(t),Ln.addKey(t,n),Ln.addValue(t,r),Ln.endKeyValue(t)}))):-1;return e.name&&(i=t.createString(e.name)),Fn.startField(t),Fn.addType(t,n),Fn.addTypeType(t,o),Fn.addChildren(t,l),Fn.addNullable(t,!!e.nullable),-1!==i&&Fn.addName(t,i),-1!==r&&Fn.addDictionary(t,r),-1!==h&&Fn.addCustomMetadata(t,h),Fn.endField(t)},Zi.decode=function(t,e){let i,n,r,s,o,a;return e&&(a=t.dictionary())?e.has(i=a.id().low)?(s=(s=a.indexType())?ls(s):new Lt,o=new Qt(e.get(i),s,i,a.isOrdered()),n=new Zi(t.name(),o,t.nullable(),as(t))):(s=(s=a.indexType())?ls(s):new Lt,e.set(i,r=hs(t,os(t,e))),o=new Qt(r,s,i,a.isOrdered()),n=new Zi(t.name(),o,t.nullable(),as(t))):(r=hs(t,os(t,e)),n=new Zi(t.name(),r,t.nullable(),as(t))),n||null},Zi.fromJSON=function(t,e){let i,n,r,s,o,a;return e&&(s=t.dictionary)?e.has(i=s.id)?(n=(n=s.indexType)?Qr(n):new Lt,a=new Qt(e.get(i),n,i,s.isOrdered),r=new Zi(t.name,a,t.nullable,Yr(t.customMetadata))):(n=(n=s.indexType)?Qr(n):new Lt,e.set(i,o=Xr(t,Wr(t,e))),a=new Qt(o,n,i,s.isOrdered),r=new Zi(t.name,a,t.nullable,Yr(t.customMetadata))):(o=Xr(t,Wr(t,e)),r=new Zi(t.name,o,t.nullable,Yr(t.customMetadata))),r||null},Gi.encode=function(t,e){const i=e.fields.map((e=>Zi.encode(t,e)));On.startFieldsVector(t,i.length);const n=On.createFieldsVector(t,i),r=e.metadata&&e.metadata.size>0?On.createCustomMetadataVector(t,[...e.metadata].map((([e,i])=>{const n=t.createString(`${e}`),r=t.createString(`${i}`);return Ln.startKeyValue(t),Ln.addKey(t,n),Ln.addValue(t,r),Ln.endKeyValue(t)}))):-1;return On.startSchema(t),On.addFields(t,n),On.addEndianness(t,cs?Tn.Little:Tn.Big),-1!==r&&On.addCustomMetadata(t,r),On.endSchema(t)},Gi.decode=function(t,e=new Map){const i=function(t,e){const i=[];for(let n,r=-1,s=-1,o=t.fieldsLength();++rZi.fromJSON(t,e)))}(t,e),Yr(t.customMetadata),e)},is.encode=function(t,e){const i=e.nodes||[],n=e.buffers||[];Sr.startNodesVector(t,i.length);for(const e of i.slice().reverse())ss.encode(t,e);const r=t.endVector();Sr.startBuffersVector(t,n.length);for(const e of n.slice().reverse())rs.encode(t,e);const s=t.endVector();return Sr.startRecordBatch(t),Sr.addLength(t,new Kr(e.length,0)),Sr.addNodes(t,r),Sr.addBuffers(t,s),Sr.endRecordBatch(t)},is.decode=function(t,i=e.V4){if(null!==t.compression())throw new Error("Record batch compression not implemented");return new is(t.length(),function(t){const e=[];for(let i,n=-1,r=-1,s=t.nodesLength();++n{const t=new ArrayBuffer(2);return new DataView(t).setInt16(0,256,!0),256===new Int16Array(t)[0]})(),us=t=>`Expected ${l[t]} Message in stream, but was null or length 0.`,ds=t=>`Header pointer of flatbuffer-encoded ${l[t]} Message is null or length 0.`,fs=(t,e)=>`Expected to read ${t} metadata bytes, but only read ${e}.`,ps=(t,e)=>`Expected to read ${t} bytes for message body, but only read ${e}.`;class gs{constructor(t){this.source=t instanceof Jn?t:new Jn(t)}[Symbol.iterator](){return this}next(){let t;return(t=this.readMetadataLength()).done||-1===t.value&&(t=this.readMetadataLength()).done||(t=this.readMetadata(t.value)).done?Zn:t}throw(t){return this.source.throw(t)}return(t){return this.source.return(t)}readMessage(t){let e;if((e=this.next()).done)return null;if(null!=t&&e.value.headerType!==t)throw new Error(us(t));return e.value}readMessageBody(t){if(t<=0)return new Uint8Array(0);const e=Y(this.source.read(t));if(e.byteLength[...e,...i.VALIDITY&&[i.VALIDITY]||[],...i.TYPE&&[i.TYPE]||[],...i.OFFSET&&[i.OFFSET]||[],...i.DATA&&[i.DATA]||[],...t(i.children)]),[])}(this._body)}readMessage(t){let e;if((e=this.next()).done)return null;if(null!=t&&e.value.headerType!==t)throw new Error(us(t));return e.value}readSchema(){const t=l.Schema,e=this.readMessage(t),i=null==e?void 0:e.header();if(!e||!i)throw new Error(ds(t));return i}}const ys=4,vs=new Uint8Array(6);for(let t=0;t<6;t+=1)vs[t]="ARROW1".codePointAt(t);function ws(t,e=0){for(let i=-1,n=vs.length;++ithis)):this}readRecordBatch(t){return this._impl.isFile()?this._impl.readRecordBatch(t):null}[Symbol.iterator](){return this._impl[Symbol.iterator]()}[Symbol.asyncIterator](){return this._impl[Symbol.asyncIterator]()}toDOMStream(){return $n.toDOMStream(this.isSync()?{[Symbol.iterator]:()=>this}:{[Symbol.asyncIterator]:()=>this})}toNodeStream(){return $n.toNodeStream(this.isSync()?{[Symbol.iterator]:()=>this}:{[Symbol.asyncIterator]:()=>this},{objectMode:!0})}static throughNode(t){throw new Error('"throughNode" not available in this environment')}static throughDOM(t,e){throw new Error('"throughDOM" not available in this environment')}static from(t){return t instanceof Ss?t:A(t)?function(t){return new Cs(new Ns(t))}(t):I(t)?function(t){return F(this,void 0,void 0,(function*(){const{size:e}=yield t.stat(),i=new rr(t,e);return e>=ks&&ws(yield i.readAt(0,_s+7&-8))?new Is(new Bs(i)):new As(new Rs(i))}))}(t):k(t)?(()=>F(this,void 0,void 0,(function*(){return yield Ss.from(yield t)})))():E(t)||R(t)||L(t)||C(t)?function(t){return F(this,void 0,void 0,(function*(){const e=yield t.peek(_s+7&-8);return e&&e.byteLength>=4?ws(e)?new Ts(new Ls(yield t.read())):new As(new Rs(t)):new As(new Rs(function(){return D(this,arguments,(function*(){}))}()))}))}(new tr(t)):function(t){const e=t.peek(_s+7&-8);return e&&e.byteLength>=4?ws(e)?new Ts(new Ls(t.read())):new Cs(new Ms(t)):new Cs(new Ms(function*(){}()))}(new Jn(t))}static readAll(t){return t instanceof Ss?t.isSync()?Os(t):Ds(t):A(t)||ArrayBuffer.isView(t)||S(t)||T(t)?Os(t):Ds(t)}}class Cs extends Ss{constructor(t){super(t),this._impl=t}readAll(){return[...this]}[Symbol.iterator](){return this._impl[Symbol.iterator]()}[Symbol.asyncIterator](){return D(this,arguments,(function*(){yield O(yield*P(z(this[Symbol.iterator]())))}))}}class As extends Ss{constructor(t){super(t),this._impl=t}readAll(){var t,e;return F(this,void 0,void 0,(function*(){const i=new Array;try{for(var n,r=z(this);!(n=yield r.next()).done;){const t=n.value;i.push(t)}}catch(e){t={error:e}}finally{try{n&&!n.done&&(e=r.return)&&(yield e.call(r))}finally{if(t)throw t.error}}return i}))}[Symbol.iterator](){throw new Error("AsyncRecordBatchStreamReader is not Iterable")}[Symbol.asyncIterator](){return this._impl[Symbol.asyncIterator]()}}class Ts extends Cs{constructor(t){super(t),this._impl=t}}class Is extends As{constructor(t){super(t),this._impl=t}}class Es{constructor(t=new Map){this.closed=!1,this.autoDestroy=!0,this._dictionaryIndex=0,this._recordBatchIndex=0,this.dictionaries=t}get numDictionaries(){return this._dictionaryIndex}get numRecordBatches(){return this._recordBatchIndex}isSync(){return!1}isAsync(){return!1}isFile(){return!1}isStream(){return!1}reset(t){return this._dictionaryIndex=0,this._recordBatchIndex=0,this.schema=t,this.dictionaries=new Map,this}_loadRecordBatch(t,e){const i=this._loadVectors(t,e,this.schema.fields),n=Wi({type:new jt(this.schema.fields),length:t.length,children:i});return new dn(this.schema,n)}_loadDictionaryBatch(t,e){const{id:i,isDelta:n}=t,{dictionaries:r,schema:s}=this,o=r.get(i);if(n||!o){const r=s.dictionaries.get(i),a=this._loadVectors(t.data,e,[r]);return(o&&n?o.concat(new Hi(a)):new Hi(a)).memoize()}return o.memoize()}_loadVectors(t,e,i){return new ur(e,t.nodes,t.buffers,this.dictionaries).visitMany(i)}}class Ms extends Es{constructor(t,e){super(e),this._reader=A(t)?new bs(this._handle=t):new gs(this._handle=t)}isSync(){return!0}isStream(){return!0}[Symbol.iterator](){return this}cancel(){!this.closed&&(this.closed=!0)&&(this.reset()._reader.return(),this._reader=null,this.dictionaries=null)}open(t){return this.closed||(this.autoDestroy=Fs(this,t),this.schema||(this.schema=this._reader.readSchema())||this.cancel()),this}throw(t){return!this.closed&&this.autoDestroy&&(this.closed=!0)?this.reset()._reader.throw(t):Zn}return(t){return!this.closed&&this.autoDestroy&&(this.closed=!0)?this.reset()._reader.return(t):Zn}next(){if(this.closed)return Zn;let t;const{_reader:e}=this;for(;t=this._readNextMessageAndValidate();)if(t.isSchema())this.reset(t.header());else{if(t.isRecordBatch()){this._recordBatchIndex++;const i=t.header(),n=e.readMessageBody(t.bodyLength);return{done:!1,value:this._loadRecordBatch(i,n)}}if(t.isDictionaryBatch()){this._dictionaryIndex++;const i=t.header(),n=e.readMessageBody(t.bodyLength),r=this._loadDictionaryBatch(i,n);this.dictionaries.set(i.id,r)}}return this.schema&&0===this._recordBatchIndex?(this._recordBatchIndex++,{done:!1,value:new gn(this.schema)}):this.return()}_readNextMessageAndValidate(t){return this._reader.readMessage(t)}}class Rs extends Es{constructor(t,e){super(e),this._reader=new ms(this._handle=t)}isAsync(){return!0}isStream(){return!0}[Symbol.asyncIterator](){return this}cancel(){return F(this,void 0,void 0,(function*(){!this.closed&&(this.closed=!0)&&(yield this.reset()._reader.return(),this._reader=null,this.dictionaries=null)}))}open(t){return F(this,void 0,void 0,(function*(){return this.closed||(this.autoDestroy=Fs(this,t),this.schema||(this.schema=yield this._reader.readSchema())||(yield this.cancel())),this}))}throw(t){return F(this,void 0,void 0,(function*(){return!this.closed&&this.autoDestroy&&(this.closed=!0)?yield this.reset()._reader.throw(t):Zn}))}return(t){return F(this,void 0,void 0,(function*(){return!this.closed&&this.autoDestroy&&(this.closed=!0)?yield this.reset()._reader.return(t):Zn}))}next(){return F(this,void 0,void 0,(function*(){if(this.closed)return Zn;let t;const{_reader:e}=this;for(;t=yield this._readNextMessageAndValidate();)if(t.isSchema())yield this.reset(t.header());else{if(t.isRecordBatch()){this._recordBatchIndex++;const i=t.header(),n=yield e.readMessageBody(t.bodyLength);return{done:!1,value:this._loadRecordBatch(i,n)}}if(t.isDictionaryBatch()){this._dictionaryIndex++;const i=t.header(),n=yield e.readMessageBody(t.bodyLength),r=this._loadDictionaryBatch(i,n);this.dictionaries.set(i.id,r)}}return this.schema&&0===this._recordBatchIndex?(this._recordBatchIndex++,{done:!1,value:new gn(this.schema)}):yield this.return()}))}_readNextMessageAndValidate(t){return F(this,void 0,void 0,(function*(){return yield this._reader.readMessage(t)}))}}class Ls extends Ms{constructor(t,e){super(t instanceof nr?t:new nr(t),e)}get footer(){return this._footer}get numDictionaries(){return this._footer?this._footer.numDictionaries:0}get numRecordBatches(){return this._footer?this._footer.numRecordBatches:0}isSync(){return!0}isFile(){return!0}open(t){if(!this.closed&&!this._footer){this.schema=(this._footer=this._readFooter()).schema;for(const 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i=document.createElement("div");t.appendChild(i),i.appendChild(yi("times")),i.addEventListener("click",(function(t){t.preventDefault(),t.stopPropagation(),e()}))}var ki=Object.freeze({__proto__:null,attachDialogCloseHandlerWithParent:xi});let Si;function Ci(t,e,i){e.addEventListener("mousedown",function(t){t.stopPropagation(),t.preventDefault();const e=Ai.bind(this),n=Ti.bind(this),r=getComputedStyle(this);Si={constraint:i,dragFunction:e,dragEndFunction:n,screenX:t.screenX,screenY:t.screenY,top:parseInt(r.top.replace("px","")),left:parseInt(r.left.replace("px",""))},document.addEventListener("mousemove",e),document.addEventListener("mouseup",n),document.addEventListener("mouseleave",n),document.addEventListener("mouseexit",n)}.bind(t))}function Ai(t){if(!Si)return void console.error("No drag data!");t.stopPropagation(),t.preventDefault();const e=t.screenX-Si.screenX,i=t.screenY-Si.screenY,n=Si.left+e,r=Si.constraint?Math.max(Si.constraint.minY,Si.top+i):Si.top+i;this.style.left=`${n}px`,this.style.top=`${r}px`}function Ti(t){if(!Si)return void console.error("No drag data!");t.stopPropagation(),t.preventDefault();const e=Si.dragFunction,i=Si.dragEndFunction;document.removeEventListener("mousemove",e),document.removeEventListener("mouseup",i),document.removeEventListener("mouseleave",i),document.removeEventListener("mouseexit",i),Si=void 0}const Ii={401:"Access unauthorized",403:"Access forbidden",404:"Not found"};class Ei{constructor(t,e){this.alertProps=Object.assign({shouldFocus:!0,preventScroll:!1},e),this.container=pe({class:"igv-ui-alert-dialog-container"}),t.appendChild(this.container),this.container.setAttribute("tabIndex","-1");const i=pe();this.container.appendChild(i),this.errorHeadline=pe(),i.appendChild(this.errorHeadline),this.errorHeadline.textContent="";let n=pe({class:"igv-ui-alert-dialog-body"});this.container.appendChild(n),this.body=pe({class:"igv-ui-alert-dialog-body-copy"}),n.appendChild(this.body);let r=pe();this.container.appendChild(r),this.ok=pe(),r.appendChild(this.ok),this.ok.textContent="OK";const s=()=>{"function"==typeof this.callback&&(this.callback("OK"),this.callback=void 0),this.body.innerHTML="",me(this.container)};this.ok.addEventListener("click",(t=>{t.stopPropagation(),s()})),this.container.addEventListener("keypress",(t=>{t.stopPropagation(),"Enter"===t.key&&s()})),Ci(this.container,i),me(this.container)}present(t,e){this.errorHeadline.textContent=t.message?"ERROR":"";let i=t.message||t;Ii.hasOwnProperty(i)&&(i=Ii[i]);const n=mi.sanitize(i);this.body.innerHTML=n,this.callback=e,be(this.container),this.alertProps.shouldFocus&&this.container.focus({preventScroll:this.alertProps.preventScroll})}}class Mi{constructor(t){this.parent=t,this.container=pe({class:"igv-ui-generic-dialog-container"}),t.appendChild(this.container);const e=pe({class:"igv-ui-generic-dialog-header"});this.container.appendChild(e),this.label=pe({class:"igv-ui-generic-dialog-one-liner"}),this.container.appendChild(this.label),this.label.text="Unlabeled",this.input_container=pe({class:"igv-ui-generic-dialog-input"}),this.container.appendChild(this.input_container),this.input=document.createElement("input"),this.input_container.appendChild(this.input);const i=pe({class:"igv-ui-generic-dialog-ok-cancel"});this.container.appendChild(i),this.ok=pe(),i.appendChild(this.ok),this.ok.textContent="OK",this.cancel=pe(),i.appendChild(this.cancel),this.cancel.textContent="Cancel",me(this.container),this.input.addEventListener("keyup",(t=>{13===t.keyCode&&("function"==typeof this.callback&&(this.callback(this.input.value),this.callback=void 0),this.input.value=void 0,me(this.container))})),this.ok.addEventListener("click",(()=>{"function"==typeof this.callback&&(this.callback(this.input.value),this.callback=void 0),this.input.value=void 0,me(this.container)}));const n=()=>{this.input.value="",me(this.container)};this.cancel.addEventListener("click",n),xi(e,n),Ci(this.container,e)}get value(){return mi.sanitize(this.input.value)}present(t,e){this.label.textContent=t.label,this.input.value=t.value,this.callback=t.callback||t.click,be(this.container),this.clampLocation(e.clientX,e.clientY)}clampLocation(t,e){const{width:i,height:n}=this.container.getBoundingClientRect(),r=window.innerHeight,s=window.innerWidth,o=Math.min(r-n,e),a=Math.min(s-i,t);this.container.style.left=`${a}px`,this.container.style.top=`${o}px`}}const Ri={licorice:"#000000",lead:"#1e1e1e",tungsten:"#3a3a3a",iron:"#545453",steel:"#6e6e6e",tin:"#878687",nickel:"#888787",aluminum:"#a09fa0",magnesium:"#b8b8b8",silver:"#d0d0d0",mercury:"#e8e8e8",snow:"#ffffff",cayenne:"#891100",mocha:"#894800",aspargus:"#888501",fern:"#458401",clover:"#028401",moss:"#018448",teal:"#008688",ocean:"#004a88",midnight:"#001888",eggplant:"#491a88",plum:"#891e88",maroon:"#891648",maraschino:"#ff2101",tangerine:"#ff8802",lemon:"#fffa03",lime:"#83f902",spring:"#05f802",seam_foam:"#03f987",turquoise:"#00fdff",aqua:"#008cff",blueberry:"#002eff",grape:"#8931ff",magenta:"#ff39ff",strawberry:"#ff2987",salmon:"#ff726e",cantaloupe:"#ffce6e",banana:"#fffb6d",honeydew:"#cefa6e",flora:"#68f96e",spindrift:"#68fbd0",ice:"#68fdff",sky:"#6acfff",orchid:"#6e76ff",lavender:"#d278ff",bubblegum:"#ff7aff",carnation:"#ff7fd3"};class Li{constructor({parent:t,top:e,left:i,width:n,height:r,border:s,closeHandler:o}){let a=pe({class:"igv-ui-generic-container"});t.appendChild(a),me(a),this.container=a,void 0!==e&&(this.container.style.top=`${e}px`),void 0!==i&&(this.container.style.left=`${i}px`),void 0!==n&&(this.container.style.width=`${n}px`),void 0!==r&&(this.container.style.height=`${r}px`),s&&(this.container.style.border=s);const l=pe();this.container.appendChild(l),xi(l,(t=>{me(this.container),"function"==typeof o&&o(t)})),Ci(this.container,l)}show(){be(this.container)}hide(){me(this.container)}dispose(){this.container.parent&&this.container.parent.removeChild(this.container)}}class Bi extends Li{constructor({parent:t,top:e,left:i,width:n,height:r,defaultColors:s,colorHandler:o}){super({parent:t,top:e,left:i,width:n,height:r,border:"1px solid gray"}),Ni(this.container,o,s)}}const Ni=(t,e,i)=>{const n=Object.values(Ri);for(let i of n){const n=pe({class:"igv-ui-color-swatch"});t.appendChild(n),Fi(n,i,e)}if(i)for(let n of i){const i=pe({class:"igv-ui-color-swatch"});t.appendChild(i),Fi(i,n,e)}},Fi=(t,e,i)=>{t.style.backgroundColor=e,t.addEventListener("mouseenter",(i=>t.style.borderColor=e)),t.addEventListener("mouseleave",(e=>t.style.borderColor="white")),t.addEventListener("click",(t=>{t.stopPropagation(),i(e)})),t.addEventListener("touchend",(t=>{t.stopPropagation(),i(e)}))};class Oi{constructor(t,e){this.parent=t,this.popover=pe({class:"igv-ui-popover"}),t.appendChild(this.popover);const i=pe();this.popover.appendChild(i);const n=pe();i.appendChild(n),e&&(n.textContent=e),xi(i,(()=>this.hide())),Ci(this.popover,i),this.popoverContent=pe(),this.popover.appendChild(this.popoverContent),this.popover.style.display="none"}presentContentWithEvent(t,e){this.popover.style.display="block",this.popoverContent.innerHTML=e,Di(t,this.popover,this.popoverContent)}presentMenu(t,e){if(0===e.length)return;this.popover.style.display="block";const i=function(t,e){const i=t.map((function(t,i){let n;if("string"==typeof t)n=pe(),n.innerHTML=t;else if("Node"==typeof t)n=t;else{if("function"==typeof t.init&&t.init(),"checkbox"===t.type)n=bi("Show all bases",t.value);else if("color"===t.type){const r=new Bi({parent:e.parentElement,width:364,colorHandler:e=>t.click(e)});n=pe(),"string"==typeof t.label&&(n.innerHTML=t.label);const s=t=>{r.show(),me(e),t.preventDefault(),t.stopPropagation()};n.addEventListener("click",s),n.addEventListener("touchend",s),n.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}else n=pe(),"string"==typeof t.label&&(n.innerHTML=t.label);if(t.click&&"color"!==t.type){function o(i){t.click(),me(e),i.preventDefault(),i.stopPropagation()}n.addEventListener("click",o),n.addEventListener("touchend",o),n.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}}return{object:n,init:t.init}}));return i}(e,this.popover);for(let t of i)this.popoverContent.appendChild(t.object);Di(t,this.popover,this.popoverContent)}hide(){this.popover.style.display="none",this.dispose()}dispose(){this.popover&&this.popover.parentNode.removeChild(this.popover);const t=Object.keys(this);for(let e of t)this[e]=void 0}}function Di(t,e,i){const{x:n,y:r,width:s}=we(t,e.parentNode);e.style.top=`${r}px`;const{width:o}=e.getBoundingClientRect(),a=n+o,l=a-s;e.style.left=`${a>s?n-l:n}px`,i.style.maxWidth=`${Math.min(o,s)}px`}class Pi extends Li{constructor({parent:t,width:e}){super({parent:t,width:e,border:"1px solid gray"})}configure(t,e){this.colorHandlers=e,this.setActiveColorHandler("color"),this.createSwatches(t)}setActiveColorHandler(t){this.activeColorHandler=this.colorHandlers[t]}createSwatches(t){this.container.querySelectorAll(".igv-ui-color-swatch").forEach((t=>t.remove()));const e=Object.values(Ri);for(let t of e){const e=pe({class:"igv-ui-color-swatch"});this.container.appendChild(e),this.decorateSwatch(e,t)}if(t)for(let e of t){const t=pe({class:"igv-ui-color-swatch"});this.container.appendChild(t),this.decorateSwatch(t,e)}}decorateSwatch(t,e){t.style.backgroundColor=e,t.addEventListener("mouseenter",(()=>t.style.borderColor=e)),t.addEventListener("mouseleave",(()=>t.style.borderColor="white")),t.addEventListener("click",(t=>{t.stopPropagation(),this.activeColorHandler(e)})),t.addEventListener("touchend",(t=>{t.stopPropagation(),this.activeColorHandler(e)}))}}if("undefined"!=typeof document){function py(t){for(let e of document.styleSheets)if(e=e.href?e.href.replace(/^.*[\\\/]/,""):"",e===t)return!0;return!1}py("igv-ui.css")||function(){const t=document.createElement("style");t.setAttribute("type","text/css"),t.setAttribute("title","igv-ui.css"),t.innerHTML='.igv-ui-popover {\n cursor: default;\n position: absolute;\n z-index: 2048;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: 1px;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n background-color: white;\n}\n.igv-ui-popover > div:first-child {\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-popover > div:first-child > div:first-child {\n margin-left: 4px;\n}\n.igv-ui-popover > div:first-child > div:last-child {\n margin-right: 4px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-ui-popover > div:first-child > div:last-child:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-ui-popover > div:last-child {\n overflow-y: auto;\n overflow-x: hidden;\n max-height: 400px;\n max-width: 800px;\n background-color: white;\n}\n.igv-ui-popover > div:last-child > div {\n user-select: all;\n margin-left: 4px;\n margin-right: 4px;\n min-width: 220px;\n overflow-x: hidden;\n text-overflow: ellipsis;\n white-space: nowrap;\n}\n.igv-ui-popover > div:last-child > div > span {\n font-weight: bolder;\n}\n.igv-ui-popover > div:last-child hr {\n width: 100%;\n}\n\n.igv-ui-alert-dialog-container {\n box-sizing: content-box;\n position: absolute;\n z-index: 2048;\n top: 50%;\n left: 50%;\n width: 400px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n outline: none;\n font-family: "Open Sans", sans-serif;\n font-size: 15px;\n font-weight: 400;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n}\n.igv-ui-alert-dialog-container > div:first-child {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-alert-dialog-container > div:first-child div:first-child {\n padding-left: 8px;\n}\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body {\n -webkit-user-select: text;\n -moz-user-select: text;\n -ms-user-select: text;\n user-select: text;\n color: #373737;\n width: 100%;\n height: calc(100% - 24px - 64px);\n overflow-y: scroll;\n}\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body .igv-ui-alert-dialog-body-copy {\n margin: 16px;\n width: auto;\n height: auto;\n overflow-wrap: break-word;\n word-break: break-word;\n background-color: white;\n border: unset;\n}\n.igv-ui-alert-dialog-container > div:last-child {\n width: 100%;\n margin-bottom: 10px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n}\n.igv-ui-alert-dialog-container > div:last-child div {\n margin: unset;\n width: 40px;\n height: 30px;\n line-height: 30px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n border-color: #2B81AF;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-ui-alert-dialog-container > div:last-child div:hover {\n cursor: pointer;\n border-color: #25597f;\n background-color: #25597f;\n}\n\n.igv-ui-color-swatch {\n position: relative;\n box-sizing: content-box;\n display: flex;\n flex-flow: row;\n flex-wrap: wrap;\n justify-content: center;\n align-items: center;\n width: 32px;\n height: 32px;\n border-style: solid;\n border-width: 2px;\n border-color: white;\n border-radius: 4px;\n}\n\n.igv-ui-color-swatch:hover {\n border-color: dimgray;\n}\n\n.igv-ui-colorpicker-menu-close-button {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 32px;\n margin-top: 4px;\n margin-bottom: 4px;\n padding-right: 8px;\n}\n.igv-ui-colorpicker-menu-close-button i.fa {\n display: block;\n margin-left: 4px;\n margin-right: 4px;\n color: #5f5f5f;\n}\n.igv-ui-colorpicker-menu-close-button i.fa:hover,\n.igv-ui-colorpicker-menu-close-button i.fa:focus,\n.igv-ui-colorpicker-menu-close-button i.fa:active {\n cursor: pointer;\n color: #0f0f0f;\n}\n\n.igv-ui-generic-dialog-container {\n box-sizing: content-box;\n position: fixed;\n top: 0;\n left: 0;\n width: 300px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n z-index: 2048;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-one-liner {\n color: #373737;\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin-top: 8px;\n padding-left: 8px;\n overflow-wrap: break-word;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input {\n margin-top: 8px;\n width: 95%;\n height: 24px;\n color: #373737;\n line-height: 24px;\n padding-left: 8px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input div {\n width: 30%;\n height: 100%;\n font-size: 16px;\n text-align: right;\n padding-right: 8px;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\n width: 50%;\n font-size: 16px;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input {\n margin-top: 8px;\n width: calc(100% - 16px);\n height: 24px;\n color: #373737;\n line-height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\n font-size: 16px;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel {\n width: 100%;\n height: 28px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div {\n margin-top: 32px;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:first-child {\n margin-left: 32px;\n margin-right: 0;\n background-color: #5ea4e0;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:last-child {\n margin-left: 0;\n margin-right: 32px;\n background-color: #c4c4c4;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f;\n}\n\n.igv-ui-generic-container {\n box-sizing: content-box;\n position: absolute;\n z-index: 2048;\n background-color: white;\n cursor: pointer;\n display: flex;\n flex-direction: row;\n flex-wrap: wrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ui-generic-container > div:first-child {\n cursor: move;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n height: 24px;\n width: 100%;\n background-color: #dddddd;\n}\n.igv-ui-generic-container > div:first-child > div {\n display: block;\n color: #5f5f5f;\n cursor: pointer;\n width: 14px;\n height: 14px;\n margin-right: 8px;\n margin-bottom: 4px;\n}\n\n.igv-ui-dialog {\n z-index: 2048;\n position: fixed;\n width: fit-content;\n height: fit-content;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n background-color: white;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n}\n.igv-ui-dialog .igv-ui-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-dialog .igv-ui-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-ui-dialog .igv-ui-dialog-header div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-ui-dialog .igv-ui-dialog-one-liner {\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin: 8px;\n overflow-wrap: break-word;\n background-color: white;\n font-weight: bold;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel {\n width: 100%;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div {\n margin: 16px;\n margin-top: 32px;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child {\n background-color: #5ea4e0;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child {\n background-color: #c4c4c4;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f;\n}\n.igv-ui-dialog .igv-ui-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-dialog .igv-ui-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-ui-dialog .igv-ui-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f;\n}\n\n.igv-ui-panel, .igv-ui-panel-row, .igv-ui-panel-column {\n z-index: 2048;\n background-color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n display: flex;\n justify-content: flex-start;\n align-items: flex-start;\n}\n\n.igv-ui-panel-column {\n display: flex;\n flex-direction: column;\n}\n\n.igv-ui-panel-row {\n display: flex;\n flex-direction: row;\n}\n\n.igv-ui-textbox {\n background-color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n display: flex;\n justify-content: flex-start;\n align-items: flex-start;\n}\n\n.igv-ui-table {\n background-color: white;\n}\n\n.igv-ui-table thead {\n position: sticky;\n top: 0;\n}\n\n.igv-ui-table th {\n text-align: left;\n}\n\n.igv-ui-table td {\n padding-right: 20px;\n}\n\n.igv-ui-table tr:hover {\n background-color: lightblue;\n}\n\n/*# sourceMappingURL=igv-ui.css.map */\n',document.head.append(t)}()}function zi(t,e){const i=_e.div({class:"igv-menu-popup-check-container"}),n=_e.div();i.appendChild(n);const r=_i.createIcon("check",!0===e?"#444":"transparent");n.appendChild(r);const s=_e.div();return 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Array(512);Ji(an);const ln=new Array(256);Ji(ln);const hn=new Array(29);Ji(hn);const cn=new Array(30);function un(t,e,i,n,r){this.static_tree=t,this.extra_bits=e,this.extra_base=i,this.elems=n,this.max_length=r,this.has_stree=t&&t.length}let dn,fn,pn;function gn(t,e){this.dyn_tree=t,this.max_code=0,this.stat_desc=e}Ji(cn);const mn=t=>t<256?an[t]:an[256+(t>>>7)],bn=(t,e)=>{t.pending_buf[t.pending++]=255&e,t.pending_buf[t.pending++]=e>>>8&255},yn=(t,e,i)=>{t.bi_valid>16-i?(t.bi_buf|=e<>16-t.bi_valid,t.bi_valid+=i-16):(t.bi_buf|=e<{yn(t,i[2*e],i[2*e+1])},wn=(t,e)=>{let i=0;do{i|=1&t,t>>>=1,i<<=1}while(--e>0);return i>>>1},_n=(t,e,i)=>{const n=new Array(16);let r,s,o=0;for(r=1;r<=15;r++)o=o+i[r-1]<<1,n[r]=o;for(s=0;s<=e;s++){let e=t[2*s+1];0!==e&&(t[2*s]=wn(n[e]++,e))}},xn=t=>{let e;for(e=0;e<286;e++)t.dyn_ltree[2*e]=0;for(e=0;e<30;e++)t.dyn_dtree[2*e]=0;for(e=0;e<19;e++)t.bl_tree[2*e]=0;t.dyn_ltree[512]=1,t.opt_len=t.static_len=0,t.sym_next=t.matches=0},kn=t=>{t.bi_valid>8?bn(t,t.bi_buf):t.bi_valid>0&&(t.pending_buf[t.pending++]=t.bi_buf),t.bi_buf=0,t.bi_valid=0},Sn=(t,e,i,n)=>{const r=2*e,s=2*i;return t[r]{const n=t.heap[i];let r=i<<1;for(;r<=t.heap_len&&(r{let n,r,s,o,a=0;if(0!==t.sym_next)do{n=255&t.pending_buf[t.sym_buf+a++],n+=(255&t.pending_buf[t.sym_buf+a++])<<8,r=t.pending_buf[t.sym_buf+a++],0===n?vn(t,r,e):(s=ln[r],vn(t,s+256+1,e),o=tn[s],0!==o&&(r-=hn[s],yn(t,r,o)),n--,s=mn(n),vn(t,s,i),o=en[s],0!==o&&(n-=cn[s],yn(t,n,o)))}while(a{const i=e.dyn_tree,n=e.stat_desc.static_tree,r=e.stat_desc.has_stree,s=e.stat_desc.elems;let o,a,l,h=-1;for(t.heap_len=0,t.heap_max=573,o=0;o>1;o>=1;o--)Cn(t,i,o);l=s;do{o=t.heap[1],t.heap[1]=t.heap[t.heap_len--],Cn(t,i,1),a=t.heap[1],t.heap[--t.heap_max]=o,t.heap[--t.heap_max]=a,i[2*l]=i[2*o]+i[2*a],t.depth[l]=(t.depth[o]>=t.depth[a]?t.depth[o]:t.depth[a])+1,i[2*o+1]=i[2*a+1]=l,t.heap[1]=l++,Cn(t,i,1)}while(t.heap_len>=2);t.heap[--t.heap_max]=t.heap[1],((t,e)=>{const i=e.dyn_tree,n=e.max_code,r=e.stat_desc.static_tree,s=e.stat_desc.has_stree,o=e.stat_desc.extra_bits,a=e.stat_desc.extra_base,l=e.stat_desc.max_length;let h,c,u,d,f,p,g=0;for(d=0;d<=15;d++)t.bl_count[d]=0;for(i[2*t.heap[t.heap_max]+1]=0,h=t.heap_max+1;h<573;h++)c=t.heap[h],d=i[2*i[2*c+1]+1]+1,d>l&&(d=l,g++),i[2*c+1]=d,c>n||(t.bl_count[d]++,f=0,c>=a&&(f=o[c-a]),p=i[2*c],t.opt_len+=p*(d+f),s&&(t.static_len+=p*(r[2*c+1]+f)));if(0!==g){do{for(d=l-1;0===t.bl_count[d];)d--;t.bl_count[d]--,t.bl_count[d+1]+=2,t.bl_count[l]--,g-=2}while(g>0);for(d=l;0!==d;d--)for(c=t.bl_count[d];0!==c;)u=t.heap[--h],u>n||(i[2*u+1]!==d&&(t.opt_len+=(d-i[2*u+1])*i[2*u],i[2*u+1]=d),c--)}})(t,e),_n(i,h,t.bl_count)},In=(t,e,i)=>{let n,r,s=-1,o=e[1],a=0,l=7,h=4;for(0===o&&(l=138,h=3),e[2*(i+1)+1]=65535,n=0;n<=i;n++)r=o,o=e[2*(n+1)+1],++a{let n,r,s=-1,o=e[1],a=0,l=7,h=4;for(0===o&&(l=138,h=3),n=0;n<=i;n++)if(r=o,o=e[2*(n+1)+1],!(++a{yn(t,0+(n?1:0),3),kn(t),bn(t,i),bn(t,~i),i&&t.pending_buf.set(t.window.subarray(e,e+i),t.pending),t.pending+=i};var Ln={_tr_init:t=>{Mn||((()=>{let t,e,i,n,r;const s=new Array(16);for(i=0,n=0;n<28;n++)for(hn[n]=i,t=0;t<1<>=7;n<30;n++)for(cn[n]=r<<7,t=0;t<1<{let r,s,o=0;t.level>0?(2===t.strm.data_type&&(t.strm.data_type=(t=>{let e,i=4093624447;for(e=0;e<=31;e++,i>>>=1)if(1&i&&0!==t.dyn_ltree[2*e])return 0;if(0!==t.dyn_ltree[18]||0!==t.dyn_ltree[20]||0!==t.dyn_ltree[26])return 1;for(e=32;e<256;e++)if(0!==t.dyn_ltree[2*e])return 1;return 0})(t)),Tn(t,t.l_desc),Tn(t,t.d_desc),o=(t=>{let e;for(In(t,t.dyn_ltree,t.l_desc.max_code),In(t,t.dyn_dtree,t.d_desc.max_code),Tn(t,t.bl_desc),e=18;e>=3&&0===t.bl_tree[2*rn[e]+1];e--);return t.opt_len+=3*(e+1)+5+5+4,e})(t),r=t.opt_len+3+7>>>3,s=t.static_len+3+7>>>3,s<=r&&(r=s)):r=s=i+5,i+4<=r&&-1!==e?Rn(t,e,i,n):4===t.strategy||s===r?(yn(t,2+(n?1:0),3),An(t,sn,on)):(yn(t,4+(n?1:0),3),((t,e,i,n)=>{let r;for(yn(t,e-257,5),yn(t,i-1,5),yn(t,n-4,4),r=0;r(t.pending_buf[t.sym_buf+t.sym_next++]=e,t.pending_buf[t.sym_buf+t.sym_next++]=e>>8,t.pending_buf[t.sym_buf+t.sym_next++]=i,0===e?t.dyn_ltree[2*i]++:(t.matches++,e--,t.dyn_ltree[2*(ln[i]+256+1)]++,t.dyn_dtree[2*mn(e)]++),t.sym_next===t.sym_end),_tr_align:t=>{yn(t,2,3),vn(t,256,sn),(t=>{16===t.bi_valid?(bn(t,t.bi_buf),t.bi_buf=0,t.bi_valid=0):t.bi_valid>=8&&(t.pending_buf[t.pending++]=255&t.bi_buf,t.bi_buf>>=8,t.bi_valid-=8)})(t)}},Bn=(t,e,i,n)=>{let r=65535&t|0,s=t>>>16&65535|0,o=0;for(;0!==i;){o=i>2e3?2e3:i,i-=o;do{r=r+e[n++]|0,s=s+r|0}while(--o);r%=65521,s%=65521}return r|s<<16|0};const Nn=new Uint32Array((()=>{let t,e=[];for(var i=0;i<256;i++){t=i;for(var n=0;n<8;n++)t=1&t?3988292384^t>>>1:t>>>1;e[i]=t}return e})());var Fn=(t,e,i,n)=>{const r=Nn,s=n+i;t^=-1;for(let i=n;i>>8^r[255&(t^e[i])];return-1^t},On={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"},Dn={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,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_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8};const{_tr_init:Pn,_tr_stored_block:zn,_tr_flush_block:Un,_tr_tally:Vn,_tr_align:Hn}=Ln,{Z_NO_FLUSH:jn,Z_PARTIAL_FLUSH:$n,Z_FULL_FLUSH:qn,Z_FINISH:Wn,Z_BLOCK:Gn,Z_OK:Zn,Z_STREAM_END:Yn,Z_STREAM_ERROR:Qn,Z_DATA_ERROR:Xn,Z_BUF_ERROR:Kn,Z_DEFAULT_COMPRESSION:Jn,Z_FILTERED:tr,Z_HUFFMAN_ONLY:er,Z_RLE:ir,Z_FIXED:nr,Z_DEFAULT_STRATEGY:rr,Z_UNKNOWN:sr,Z_DEFLATED:or}=Dn,ar=258,lr=262,hr=42,cr=113,ur=666,dr=(t,e)=>(t.msg=On[e],e),fr=t=>2*t-(t>4?9:0),pr=t=>{let e=t.length;for(;--e>=0;)t[e]=0},gr=t=>{let e,i,n,r=t.w_size;e=t.hash_size,n=e;do{i=t.head[--n],t.head[n]=i>=r?i-r:0}while(--e);e=r,n=e;do{i=t.prev[--n],t.prev[n]=i>=r?i-r:0}while(--e)};let mr=(t,e,i)=>(e<{const e=t.state;let i=e.pending;i>t.avail_out&&(i=t.avail_out),0!==i&&(t.output.set(e.pending_buf.subarray(e.pending_out,e.pending_out+i),t.next_out),t.next_out+=i,e.pending_out+=i,t.total_out+=i,t.avail_out-=i,e.pending-=i,0===e.pending&&(e.pending_out=0))},yr=(t,e)=>{Un(t,t.block_start>=0?t.block_start:-1,t.strstart-t.block_start,e),t.block_start=t.strstart,br(t.strm)},vr=(t,e)=>{t.pending_buf[t.pending++]=e},wr=(t,e)=>{t.pending_buf[t.pending++]=e>>>8&255,t.pending_buf[t.pending++]=255&e},_r=(t,e,i,n)=>{let r=t.avail_in;return r>n&&(r=n),0===r?0:(t.avail_in-=r,e.set(t.input.subarray(t.next_in,t.next_in+r),i),1===t.state.wrap?t.adler=Bn(t.adler,e,r,i):2===t.state.wrap&&(t.adler=Fn(t.adler,e,r,i)),t.next_in+=r,t.total_in+=r,r)},xr=(t,e)=>{let i,n,r=t.max_chain_length,s=t.strstart,o=t.prev_length,a=t.nice_match;const l=t.strstart>t.w_size-lr?t.strstart-(t.w_size-lr):0,h=t.window,c=t.w_mask,u=t.prev,d=t.strstart+ar;let f=h[s+o-1],p=h[s+o];t.prev_length>=t.good_match&&(r>>=2),a>t.lookahead&&(a=t.lookahead);do{if(i=e,h[i+o]===p&&h[i+o-1]===f&&h[i]===h[s]&&h[++i]===h[s+1]){s+=2,i++;do{}while(h[++s]===h[++i]&&h[++s]===h[++i]&&h[++s]===h[++i]&&h[++s]===h[++i]&&h[++s]===h[++i]&&h[++s]===h[++i]&&h[++s]===h[++i]&&h[++s]===h[++i]&&so){if(t.match_start=e,o=n,n>=a)break;f=h[s+o-1],p=h[s+o]}}}while((e=u[e&c])>l&&0!=--r);return o<=t.lookahead?o:t.lookahead},kr=t=>{const e=t.w_size;let i,n,r;do{if(n=t.window_size-t.lookahead-t.strstart,t.strstart>=e+(e-lr)&&(t.window.set(t.window.subarray(e,e+e-n),0),t.match_start-=e,t.strstart-=e,t.block_start-=e,t.insert>t.strstart&&(t.insert=t.strstart),gr(t),n+=e),0===t.strm.avail_in)break;if(i=_r(t.strm,t.window,t.strstart+t.lookahead,n),t.lookahead+=i,t.lookahead+t.insert>=3)for(r=t.strstart-t.insert,t.ins_h=t.window[r],t.ins_h=mr(t,t.ins_h,t.window[r+1]);t.insert&&(t.ins_h=mr(t,t.ins_h,t.window[r+3-1]),t.prev[r&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=r,r++,t.insert--,!(t.lookahead+t.insert<3)););}while(t.lookahead{let i,n,r,s=t.pending_buf_size-5>t.w_size?t.w_size:t.pending_buf_size-5,o=0,a=t.strm.avail_in;do{if(i=65535,r=t.bi_valid+42>>3,t.strm.avail_outn+t.strm.avail_in&&(i=n+t.strm.avail_in),i>r&&(i=r),i>8,t.pending_buf[t.pending-2]=~i,t.pending_buf[t.pending-1]=~i>>8,br(t.strm),n&&(n>i&&(n=i),t.strm.output.set(t.window.subarray(t.block_start,t.block_start+n),t.strm.next_out),t.strm.next_out+=n,t.strm.avail_out-=n,t.strm.total_out+=n,t.block_start+=n,i-=n),i&&(_r(t.strm,t.strm.output,t.strm.next_out,i),t.strm.next_out+=i,t.strm.avail_out-=i,t.strm.total_out+=i)}while(0===o);return a-=t.strm.avail_in,a&&(a>=t.w_size?(t.matches=2,t.window.set(t.strm.input.subarray(t.strm.next_in-t.w_size,t.strm.next_in),0),t.strstart=t.w_size,t.insert=t.strstart):(t.window_size-t.strstart<=a&&(t.strstart-=t.w_size,t.window.set(t.window.subarray(t.w_size,t.w_size+t.strstart),0),t.matches<2&&t.matches++,t.insert>t.strstart&&(t.insert=t.strstart)),t.window.set(t.strm.input.subarray(t.strm.next_in-a,t.strm.next_in),t.strstart),t.strstart+=a,t.insert+=a>t.w_size-t.insert?t.w_size-t.insert:a),t.block_start=t.strstart),t.high_waterr&&t.block_start>=t.w_size&&(t.block_start-=t.w_size,t.strstart-=t.w_size,t.window.set(t.window.subarray(t.w_size,t.w_size+t.strstart),0),t.matches<2&&t.matches++,r+=t.w_size,t.insert>t.strstart&&(t.insert=t.strstart)),r>t.strm.avail_in&&(r=t.strm.avail_in),r&&(_r(t.strm,t.window,t.strstart,r),t.strstart+=r,t.insert+=r>t.w_size-t.insert?t.w_size-t.insert:r),t.high_water>3,r=t.pending_buf_size-r>65535?65535:t.pending_buf_size-r,s=r>t.w_size?t.w_size:r,n=t.strstart-t.block_start,(n>=s||(n||e===Wn)&&e!==jn&&0===t.strm.avail_in&&n<=r)&&(i=n>r?r:n,o=e===Wn&&0===t.strm.avail_in&&i===n?1:0,zn(t,t.block_start,i,o),t.block_start+=i,br(t.strm)),o?3:1)},Cr=(t,e)=>{let i,n;for(;;){if(t.lookahead=3&&(t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart),0!==i&&t.strstart-i<=t.w_size-lr&&(t.match_length=xr(t,i)),t.match_length>=3)if(n=Vn(t,t.strstart-t.match_start,t.match_length-3),t.lookahead-=t.match_length,t.match_length<=t.max_lazy_match&&t.lookahead>=3){t.match_length--;do{t.strstart++,t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart}while(0!=--t.match_length);t.strstart++}else t.strstart+=t.match_length,t.match_length=0,t.ins_h=t.window[t.strstart],t.ins_h=mr(t,t.ins_h,t.window[t.strstart+1]);else n=Vn(t,0,t.window[t.strstart]),t.lookahead--,t.strstart++;if(n&&(yr(t,!1),0===t.strm.avail_out))return 1}return t.insert=t.strstart<2?t.strstart:2,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2},Ar=(t,e)=>{let i,n,r;for(;;){if(t.lookahead=3&&(t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart),t.prev_length=t.match_length,t.prev_match=t.match_start,t.match_length=2,0!==i&&t.prev_length4096)&&(t.match_length=2)),t.prev_length>=3&&t.match_length<=t.prev_length){r=t.strstart+t.lookahead-3,n=Vn(t,t.strstart-1-t.prev_match,t.prev_length-3),t.lookahead-=t.prev_length-1,t.prev_length-=2;do{++t.strstart<=r&&(t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart)}while(0!=--t.prev_length);if(t.match_available=0,t.match_length=2,t.strstart++,n&&(yr(t,!1),0===t.strm.avail_out))return 1}else if(t.match_available){if(n=Vn(t,0,t.window[t.strstart-1]),n&&yr(t,!1),t.strstart++,t.lookahead--,0===t.strm.avail_out)return 1}else t.match_available=1,t.strstart++,t.lookahead--}return t.match_available&&(n=Vn(t,0,t.window[t.strstart-1]),t.match_available=0),t.insert=t.strstart<2?t.strstart:2,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2};function Tr(t,e,i,n,r){this.good_length=t,this.max_lazy=e,this.nice_length=i,this.max_chain=n,this.func=r}const Ir=[new Tr(0,0,0,0,Sr),new Tr(4,4,8,4,Cr),new Tr(4,5,16,8,Cr),new Tr(4,6,32,32,Cr),new Tr(4,4,16,16,Ar),new Tr(8,16,32,32,Ar),new Tr(8,16,128,128,Ar),new Tr(8,32,128,256,Ar),new Tr(32,128,258,1024,Ar),new Tr(32,258,258,4096,Ar)];function Er(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=or,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(1146),this.dyn_dtree=new Uint16Array(122),this.bl_tree=new Uint16Array(78),pr(this.dyn_ltree),pr(this.dyn_dtree),pr(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(16),this.heap=new Uint16Array(573),pr(this.heap),this.heap_len=0,this.heap_max=0,this.depth=new Uint16Array(573),pr(this.depth),this.sym_buf=0,this.lit_bufsize=0,this.sym_next=0,this.sym_end=0,this.opt_len=0,this.static_len=0,this.matches=0,this.insert=0,this.bi_buf=0,this.bi_valid=0}const Mr=t=>{if(!t)return 1;const e=t.state;return!e||e.strm!==t||e.status!==hr&&57!==e.status&&69!==e.status&&73!==e.status&&91!==e.status&&103!==e.status&&e.status!==cr&&e.status!==ur?1:0},Rr=t=>{if(Mr(t))return dr(t,Qn);t.total_in=t.total_out=0,t.data_type=sr;const e=t.state;return e.pending=0,e.pending_out=0,e.wrap<0&&(e.wrap=-e.wrap),e.status=2===e.wrap?57:e.wrap?hr:cr,t.adler=2===e.wrap?0:1,e.last_flush=-2,Pn(e),Zn},Lr=t=>{const e=Rr(t);var i;return e===Zn&&((i=t.state).window_size=2*i.w_size,pr(i.head),i.max_lazy_match=Ir[i.level].max_lazy,i.good_match=Ir[i.level].good_length,i.nice_match=Ir[i.level].nice_length,i.max_chain_length=Ir[i.level].max_chain,i.strstart=0,i.block_start=0,i.lookahead=0,i.insert=0,i.match_length=i.prev_length=2,i.match_available=0,i.ins_h=0),e},Br=(t,e,i,n,r,s)=>{if(!t)return Qn;let o=1;if(e===Jn&&(e=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||i!==or||n<8||n>15||e<0||e>9||s<0||s>nr||8===n&&1!==o)return dr(t,Qn);8===n&&(n=9);const a=new Er;return t.state=a,a.strm=t,a.status=hr,a.wrap=o,a.gzhead=null,a.w_bits=n,a.w_size=1<Br(t,e,or,15,8,rr),deflateInit2:Br,deflateReset:Lr,deflateResetKeep:Rr,deflateSetHeader:(t,e)=>Mr(t)||2!==t.state.wrap?Qn:(t.state.gzhead=e,Zn),deflate:(t,e)=>{if(Mr(t)||e>Gn||e<0)return t?dr(t,Qn):Qn;const i=t.state;if(!t.output||0!==t.avail_in&&!t.input||i.status===ur&&e!==Wn)return dr(t,0===t.avail_out?Kn:Qn);const n=i.last_flush;if(i.last_flush=e,0!==i.pending){if(br(t),0===t.avail_out)return i.last_flush=-1,Zn}else if(0===t.avail_in&&fr(e)<=fr(n)&&e!==Wn)return dr(t,Kn);if(i.status===ur&&0!==t.avail_in)return dr(t,Kn);if(i.status===hr&&0===i.wrap&&(i.status=cr),i.status===hr){let e=or+(i.w_bits-8<<4)<<8,n=-1;if(n=i.strategy>=er||i.level<2?0:i.level<6?1:6===i.level?2:3,e|=n<<6,0!==i.strstart&&(e|=32),e+=31-e%31,wr(i,e),0!==i.strstart&&(wr(i,t.adler>>>16),wr(i,65535&t.adler)),t.adler=1,i.status=cr,br(t),0!==i.pending)return i.last_flush=-1,Zn}if(57===i.status)if(t.adler=0,vr(i,31),vr(i,139),vr(i,8),i.gzhead)vr(i,(i.gzhead.text?1:0)+(i.gzhead.hcrc?2:0)+(i.gzhead.extra?4:0)+(i.gzhead.name?8:0)+(i.gzhead.comment?16:0)),vr(i,255&i.gzhead.time),vr(i,i.gzhead.time>>8&255),vr(i,i.gzhead.time>>16&255),vr(i,i.gzhead.time>>24&255),vr(i,9===i.level?2:i.strategy>=er||i.level<2?4:0),vr(i,255&i.gzhead.os),i.gzhead.extra&&i.gzhead.extra.length&&(vr(i,255&i.gzhead.extra.length),vr(i,i.gzhead.extra.length>>8&255)),i.gzhead.hcrc&&(t.adler=Fn(t.adler,i.pending_buf,i.pending,0)),i.gzindex=0,i.status=69;else if(vr(i,0),vr(i,0),vr(i,0),vr(i,0),vr(i,0),vr(i,9===i.level?2:i.strategy>=er||i.level<2?4:0),vr(i,3),i.status=cr,br(t),0!==i.pending)return i.last_flush=-1,Zn;if(69===i.status){if(i.gzhead.extra){let e=i.pending,n=(65535&i.gzhead.extra.length)-i.gzindex;for(;i.pending+n>i.pending_buf_size;){let r=i.pending_buf_size-i.pending;if(i.pending_buf.set(i.gzhead.extra.subarray(i.gzindex,i.gzindex+r),i.pending),i.pending=i.pending_buf_size,i.gzhead.hcrc&&i.pending>e&&(t.adler=Fn(t.adler,i.pending_buf,i.pending-e,e)),i.gzindex+=r,br(t),0!==i.pending)return i.last_flush=-1,Zn;e=0,n-=r}let r=new Uint8Array(i.gzhead.extra);i.pending_buf.set(r.subarray(i.gzindex,i.gzindex+n),i.pending),i.pending+=n,i.gzhead.hcrc&&i.pending>e&&(t.adler=Fn(t.adler,i.pending_buf,i.pending-e,e)),i.gzindex=0}i.status=73}if(73===i.status){if(i.gzhead.name){let e,n=i.pending;do{if(i.pending===i.pending_buf_size){if(i.gzhead.hcrc&&i.pending>n&&(t.adler=Fn(t.adler,i.pending_buf,i.pending-n,n)),br(t),0!==i.pending)return i.last_flush=-1,Zn;n=0}e=i.gzindexn&&(t.adler=Fn(t.adler,i.pending_buf,i.pending-n,n)),i.gzindex=0}i.status=91}if(91===i.status){if(i.gzhead.comment){let e,n=i.pending;do{if(i.pending===i.pending_buf_size){if(i.gzhead.hcrc&&i.pending>n&&(t.adler=Fn(t.adler,i.pending_buf,i.pending-n,n)),br(t),0!==i.pending)return i.last_flush=-1,Zn;n=0}e=i.gzindexn&&(t.adler=Fn(t.adler,i.pending_buf,i.pending-n,n))}i.status=103}if(103===i.status){if(i.gzhead.hcrc){if(i.pending+2>i.pending_buf_size&&(br(t),0!==i.pending))return i.last_flush=-1,Zn;vr(i,255&t.adler),vr(i,t.adler>>8&255),t.adler=0}if(i.status=cr,br(t),0!==i.pending)return i.last_flush=-1,Zn}if(0!==t.avail_in||0!==i.lookahead||e!==jn&&i.status!==ur){let n=0===i.level?Sr(i,e):i.strategy===er?((t,e)=>{let i;for(;;){if(0===t.lookahead&&(kr(t),0===t.lookahead)){if(e===jn)return 1;break}if(t.match_length=0,i=Vn(t,0,t.window[t.strstart]),t.lookahead--,t.strstart++,i&&(yr(t,!1),0===t.strm.avail_out))return 1}return t.insert=0,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2})(i,e):i.strategy===ir?((t,e)=>{let i,n,r,s;const o=t.window;for(;;){if(t.lookahead<=ar){if(kr(t),t.lookahead<=ar&&e===jn)return 1;if(0===t.lookahead)break}if(t.match_length=0,t.lookahead>=3&&t.strstart>0&&(r=t.strstart-1,n=o[r],n===o[++r]&&n===o[++r]&&n===o[++r])){s=t.strstart+ar;do{}while(n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&rt.lookahead&&(t.match_length=t.lookahead)}if(t.match_length>=3?(i=Vn(t,1,t.match_length-3),t.lookahead-=t.match_length,t.strstart+=t.match_length,t.match_length=0):(i=Vn(t,0,t.window[t.strstart]),t.lookahead--,t.strstart++),i&&(yr(t,!1),0===t.strm.avail_out))return 1}return t.insert=0,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2})(i,e):Ir[i.level].func(i,e);if(3!==n&&4!==n||(i.status=ur),1===n||3===n)return 0===t.avail_out&&(i.last_flush=-1),Zn;if(2===n&&(e===$n?Hn(i):e!==Gn&&(zn(i,0,0,!1),e===qn&&(pr(i.head),0===i.lookahead&&(i.strstart=0,i.block_start=0,i.insert=0))),br(t),0===t.avail_out))return i.last_flush=-1,Zn}return e!==Wn?Zn:i.wrap<=0?Yn:(2===i.wrap?(vr(i,255&t.adler),vr(i,t.adler>>8&255),vr(i,t.adler>>16&255),vr(i,t.adler>>24&255),vr(i,255&t.total_in),vr(i,t.total_in>>8&255),vr(i,t.total_in>>16&255),vr(i,t.total_in>>24&255)):(wr(i,t.adler>>>16),wr(i,65535&t.adler)),br(t),i.wrap>0&&(i.wrap=-i.wrap),0!==i.pending?Zn:Yn)},deflateEnd:t=>{if(Mr(t))return Qn;const e=t.state.status;return t.state=null,e===cr?dr(t,Xn):Zn},deflateSetDictionary:(t,e)=>{let i=e.length;if(Mr(t))return Qn;const n=t.state,r=n.wrap;if(2===r||1===r&&n.status!==hr||n.lookahead)return Qn;if(1===r&&(t.adler=Bn(t.adler,e,i,0)),n.wrap=0,i>=n.w_size){0===r&&(pr(n.head),n.strstart=0,n.block_start=0,n.insert=0);let t=new Uint8Array(n.w_size);t.set(e.subarray(i-n.w_size,i),0),e=t,i=n.w_size}const s=t.avail_in,o=t.next_in,a=t.input;for(t.avail_in=i,t.next_in=0,t.input=e,kr(n);n.lookahead>=3;){let t=n.strstart,e=n.lookahead-2;do{n.ins_h=mr(n,n.ins_h,n.window[t+3-1]),n.prev[t&n.w_mask]=n.head[n.ins_h],n.head[n.ins_h]=t,t++}while(--e);n.strstart=t,n.lookahead=2,kr(n)}return n.strstart+=n.lookahead,n.block_start=n.strstart,n.insert=n.lookahead,n.lookahead=0,n.match_length=n.prev_length=2,n.match_available=0,t.next_in=o,t.input=a,t.avail_in=s,n.wrap=r,Zn},deflateInfo:"pako deflate (from Nodeca project)"};const Fr=(t,e)=>Object.prototype.hasOwnProperty.call(t,e);var Or={assign:function(t){const e=Array.prototype.slice.call(arguments,1);for(;e.length;){const i=e.shift();if(i){if("object"!=typeof i)throw new TypeError(i+"must be non-object");for(const e in i)Fr(i,e)&&(t[e]=i[e])}}return t},flattenChunks:t=>{let e=0;for(let i=0,n=t.length;i=252?6:my>=248?5:my>=240?4:my>=224?3:my>=192?2:1;Pr[254]=Pr[254]=1;var zr={string2buf:t=>{if("function"==typeof TextEncoder&&TextEncoder.prototype.encode)return(new TextEncoder).encode(t);let 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i.next_out>0&&this.onData(i.output.subarray(0,i.next_out)),r=Nr.deflateEnd(this.strm),this.onEnd(r),this.ended=!0,r===Wr;if(0!==i.avail_out){if(s>0&&i.next_out>0)this.onData(i.output.subarray(0,i.next_out)),i.avail_out=0;else if(0===i.avail_in)break}else this.onData(i.output)}return!0},Xr.prototype.onData=function(t){this.chunks.push(t)},Xr.prototype.onEnd=function(t){t===Wr&&(this.result=Or.flattenChunks(this.chunks)),this.chunks=[],this.err=t,this.msg=this.strm.msg};var Jr={Deflate:Xr,deflate:Kr,deflateRaw:function(t,e){return(e=e||{}).raw=!0,Kr(t,e)},gzip:function(t,e){return(e=e||{}).gzip=!0,Kr(t,e)},constants:Dn};const ts=16209;var es=function(t,e){let i,n,r,s,o,a,l,h,c,u,d,f,p,g,m,b,y,v,w,_,x,k,S,C;const 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this.readSequence(t,n,r);this.interval=new Da(t,n,r,s)}const n=e-this.interval.start,r=i-e;return this.interval.features?this.interval.features.substr(n,r):null}async getIndex(){if(this.index)return this.index;{const t=await zo.load(this.indexFile,la(this.config)),e=Pa(t),i=e.length;let n=0,r=0;for(this.index={};nthis.compressedIndex[n][1])return[n];let r=0,s=n,o=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,l=!1;for(let e=0;et){l=!0;break}e=e));t++);const h=i[i.length-1];return h===this.compressedIndex.length-1&&this.compressedIndex[h][1]0&&(b=Math.min(s-r,a-d),y+=m.substr(v,b),v+=b+h);v{this.reversed=!this.reversed,this.trackView.repaintViews()}},{name:this.frameTranslate?"Close Translation":"Three-frame Translate",click:()=>{if(this.frameTranslate=!this.frameTranslate,this.frameTranslate){for(let t of this.trackView.viewports)t.setContentHeight(Qa);this.trackView.setTrackHeight(Qa)}else{for(let t of this.trackView.viewports)t.setContentHeight(25);this.trackView.setTrackHeight(25)}this.trackView.repaintViews()}}]}contextMenuItemList(t){const e=t.viewport;if(e.referenceFrame.bpPerPixel<=1){const t=e.getWidth()*e.referenceFrame.bpPerPixel,i=e.referenceFrame.chr,n=Math.floor(e.referenceFrame.start),r=Math.ceil(n+t),s=[{label:this.reversed?"View visible sequence (reversed)...":"View visible sequence...",click:async()=>{let t=await this.browser.genome.sequence.getSequence(i,n,r);t?this.reversed&&(t=Ra(t)):t="Unknown sequence",this.browser.alert.present(t)}}];return ba()&&s.push({label:"Copy visible sequence",click:async()=>{let t=await this.browser.genome.sequence.getSequence(i,n,r);t?this.reversed&&(t=Ra(t)):t="Unknown sequence";try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),s.push("
"),s}}translateSequence(t){const e=[[],[],[]];for(let i of[0,1,2]){let n=i;for(;t.length-n>=3;){let r=t.slice(n,n+3);this.reversed&&(r=r.split("").reverse().join(""));const s=Wa[r.toUpperCase()]||"";e[i].push({codons:r,aminoA:s}),n+=3}}return e}async getSequenceSource(){return this.config.fastaURL?(this.fasta||(this.fasta=new Ka(this.config,this.browser.genome),await this.fasta.init()),this.fasta):this.browser.genome.sequence}async getFeatures(t,e,i,n){if(e=Math.floor(e),i=Math.floor(i),n&&n>10)return null;{const n=await this.getSequenceSource();return{bpStart:e,sequence:await n.getSequence(t,e,i)}}}draw(t){const e=t.context;if(t.features){let i=t.features.sequence;if(!i)return;this.reversed&&(i=i.split("").map((function(t){return Ga[t]})).join(""));const n=t.features.bpStart,r=1+t.bpStart+t.pixelWidth*t.bpPerPixel;for(let s=Math.floor(t.bpStart);s<=r;s++){const r=Math.floor(s-n);if(r>=0&&r.1)na.fillRect(e,n,5,o,10,{fillStyle:l});else{const i=n+.5*(o-e.measureText(a).width);"y"===t.axis?(e.save(),na.labelTransformWithContext(e,i),na.strokeText(e,a,i,15,{strokeStyle:l}),e.restore()):na.strokeText(e,a,i,15,{strokeStyle:l})}}}if(this.frameTranslate){let r=25;const s=this.translateSequence(i);for(let i=0;it.pixelWidth)break;let f=l.aminoA;l.aminoA.indexOf("STOP")>-1?(a="rgb(255, 0, 0)",f="STOP"):"M"===l.aminoA&&(a="rgb(0, 153, 0)",f="START"),na.fillRect(e,c,r,u-c,25,{fillStyle:a}),t.bpPerPixel<=.1&&na.strokeText(e,f,d-e.measureText(f).width/2,r+15)}r+=30}}}}get supportsWholeGenome(){return!1}computePixelHeight(t){return this.height=this.frameTranslate?Qa:25,this.height}fillColor(t){return this.color?this.color:"dna"===this.sequenceType?$a[t]||"gray":"rgb(0, 0, 150)"}getState(){const t={type:"sequence"};return this.order!==qa&&(t.order=this.order),this.reversed&&(t.revealed=!0),t}}class Ka{constructor(t,e){this.config=t,this.genome=e}async init(){this.fasta=await ja(this.config),this.chrNameMap=new Map;for(let t of this.fasta.chromosomeNames)this.chrNameMap.set(this.genome.getChromosomeName(t),t)}async getSequence(t,e,i){const n=this.chrNameMap.has(t)?this.chrNameMap.get(t):t;return this.fasta.getSequence(n,e,i)}}class Ja{constructor(t,e,i,n){this.guid=_e.guid(),this.trackView=t,this.referenceFrame=i,this.browser=t.browser,this.$viewport=fe('
'),e.appendChild(this.$viewport.get(0)),t.track.height&&(this.$viewport.get(0).style.height=`${t.track.height}px`),t.track instanceof Xa&&(this.alert=new Ei(this.$viewport.get(0))),this.contentTop=0,this.contentHeight=this.$viewport.height(),this.$viewport.width(n),this.initializationHelper()}initializationHelper(){}showMessage(t){this.messageDiv||(this.messageDiv=document.createElement("div"),this.messageDiv.className="igv-viewport-message",this.$viewport.append(fe(this.messageDiv))),this.messageDiv.textContent=t,this.messageDiv.style.display="inline-block"}hideMessage(t){this.messageDiv&&(this.messageDiv.style.display="none")}setTrackLabel(t){}startSpinner(){}stopSpinner(){}checkZoomIn(){return!0}shift(){}setTop(t){this.contentTop=t,this.$viewport.height()}async loadFeatures(){}clearCache(){}async repaint(){}draw(t,e,i){console.log("Viewport - draw(drawConfiguration, features, roiFeatures)")}checkContentHeight(t){let e=this.trackView.track;if(t=t||this.cachedFeatures,"FILL"===e.displayMode)this.setContentHeight(this.$viewport.height());else if("function"==typeof e.computePixelHeight&&t&&t.length>0){let i=e.computePixelHeight(t);i!==this.contentHeight&&this.setContentHeight(i)}}getContentHeight(){return this.contentHeight}setContentHeight(t){this.contentHeight=t}isLoading(){return!1}saveSVG(){}isVisible(){return this.$viewport.width()}setWidth(t){this.$viewport.width(t)}getWidth(){return this.$viewport.width()}getContentTop(){return this.contentTop}containsPosition(t,e){console.log("Viewport - containsPosition(chr, position)")}addMouseHandlers(){}removeMouseHandlers(){}dispose(){this.popover&&this.popover.dispose(),this.$viewport.get(0).remove();for(let t of Object.keys(this))this[t]=void 0}}function tl(t,e){var 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0===e&&(e=t),this.__addTransform(tl("scale({x},{y})",{x:t,y:e}))}rotate(t){var e=180*t/Math.PI;this.__addTransform(tl("rotate({angle},{cx},{cy})",{angle:e,cx:0,cy:0}))}translate(t,e){this.__addTransform(tl("translate({x},{y})",{x:t,y:e}))}transform(t,e,i,n,r,s){this.__addTransform(tl("matrix({a},{b},{c},{d},{e},{f})",{a:t,b:e,c:i,d:n,e:r,f:s}))}beginPath(){var t;this.__currentDefaultPath="",this.__currentPosition={},t=this.__createElement("path",{},!0),this.__closestGroupOrSvg().appendChild(t),this.__currentElement=t}__applyCurrentDefaultPath(){var t=this.__currentElement;"path"===t.nodeName?t.setAttribute("d",this.__currentDefaultPath):console.error("Attempted to apply path command to node",t.nodeName)}__addPathCommand(t){this.__currentDefaultPath+=" ",this.__currentDefaultPath+=t}moveTo(t,e){"path"!==this.__currentElement.nodeName&&this.beginPath(),this.__currentPosition={x:t,y:e},this.__addPathCommand(tl("M {x} 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n.setAttribute("id",r),n.setAttribute("width",t.width),n.setAttribute("height",t.height),"CANVAS"===t.nodeName||"IMG"===t.nodeName?(i=this.__createElement("image"),i.setAttribute("width",t.width),i.setAttribute("height",t.height),i.setAttributeNS("http://www.w3.org/1999/xlink","xlink:href","CANVAS"===t.nodeName?t.toDataURL():t.getAttribute("src")),n.appendChild(i),this.__defs.appendChild(n)):t instanceof ll&&(n.appendChild(t.__root.childNodes[1]),this.__defs.appendChild(n)),new al(n,this)}setLineDash(t){t&&t.length>0?this.lineDash=t.join(","):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}const hl=function(t,e,i,n){this.start=t,this.end=e,this.name=i,this.stain=0,"acen"===n?this.type="c":(this.type=n.charAt(1),"p"===this.type&&(this.stain=parseInt(n.substring(4))))};const cl=qi,ul={loadGenome:async function(t){const e=t.cytobandURL,i=t.aliasURL,n=await ja(t);let r;i&&(r=await function(t,e){return zo.loadString(t,la(e)).then((function(t){var e=cl(t),i=[];return e.forEach((function(t){!t.startsWith("#")&&t.length>0&&i.push(t.split("\t"))})),i}))}(i,n.config));const s=new dl(t,n,r);return e&&(s.cytobands=await async function(t,e,i){let n;if(fa(t)){const e=bo(t);n="";const i=e.length;for(let t=0;t1?function(t,e){let i;if(e.chromosomeOrder)Array.isArray(e.chromosomeOrder)?t.wgChromosomeNames=e.chromosomeOrder:t.wgChromosomeNames=e.chromosomeOrder.split(",").map((t=>t.trim())),i=t.wgChromosomeNames.map((e=>t.chromosomes[e])).filter((t=>void 0!==t));else{const e=Object.keys(t.chromosomes).map((e=>t.chromosomes[e].bpLength)).reduce(((t,e)=>Math.max(t,e)))/50;i=Object.values(t.chromosomes).filter((t=>t.bpLength>e));const n=i.filter((t=>r(t.name.replace("chr","")))),s=i.filter((t=>!r(t.name.replace("chr",""))));n.sort(((t,e)=>Number.parseInt(t.name.replace("chr",""))-Number.parseInt(e.name.replace("chr",""))));const o=n.map((t=>t.name));for(let t of s)o.push(t.name);t.wgChromosomeNames=o}const n=i.reduce(((t,e)=>t+e.bpLength),0);function r(t){return/^\d+$/.test(t)}t.chromosomes.all={name:"all",bpLength:n}}(this,t):this.wgChromosomeNames=e.chromosomeNames;var n={},r=this;n.all="all",this.chromosomeNames.forEach((function(t){var e=t.startsWith("chr")?t.substring(3):"chr"+t;n[e.toLowerCase()]=t,"chrM"===t&&(n.mt="chrM"),"MT"===t&&(n.chrm="MT"),n[t.toLowerCase()]=t})),i&&i.forEach((function(t){var e,i;for(i=0;it.bpLength)&&(t=i)}return t}}getChromosomes(){return this.chromosomes}getGenomeCoordinate(t,e){var i=this.getCumulativeOffset(t);if(void 0!==i)return i+e}getChromosomeCoordinate(t){let e;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let i=0;for(let n of this.wgChromosomeNames){const r=this.cumulativeOffsets[n];if(r>t)return{chr:e,position:t-i};e=n,i=r}return{chr:this.wgChromosomeNames[this.wgChromosomeNames.length-1],position:0}}getCumulativeOffset(t){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let t=this,e={},i=0;for(let n of t.wgChromosomeNames)e[n]=Math.floor(i),i+=t.getChromosome(n).bpLength;return e}.call(this));const e=this.getChromosomeName(t);return this.cumulativeOffsets[e]}getGenomeLength(){let t=this;if(!this.bpLength){let e=0;t.wgChromosomeNames.forEach((function(i){let n=t.chromosomes[i];e+=n.bpLength})),this.bpLength=e}return this.bpLength}async getSequence(t,e,i){return t=this.getChromosomeName(t),this.sequence.getSequence(t,e,i)}addFeaturesToDB(t,e){const i=(t,e)=>{const i=this.featureDB.get(t);i&&(e=e.end-e.start>i.end-i.start?e:i),this.featureDB.set(t,e)};for(let n of t)if(n.name&&i(n.name.toUpperCase(),n),n.gene&&n.gene.name&&i(n.gene.name.toUpperCase(),n),e.searchableFields)for(let t of e.searchableFields){const e=n.getAttributeValue(t);e&&(e.indexOf(" ")>0?i(e.replaceAll(" ","+").toUpperCase(),n):i(e.toUpperCase(),n))}}}let fl,pl=0,gl=0;class ml extends Ja{constructor(t,e,i,n){super(t,e,i,n)}initializationHelper(){this.$spinner=fe("
",{class:"igv-loading-spinner-container"}),this.$viewport.append(this.$spinner),this.$spinner.append(fe("
"));const t=this.trackView.track;"sequence"!==t.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$viewport)),t.name&&"sequence"!==t.id&&(this.$trackLabel=fe('
'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(t.name),!1===this.browser.trackLabelsVisible&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(t){super.setContentHeight(t),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(t){this.$trackLabel.empty(),this.$trackLabel.html(t);const e=this.$trackLabel.text();this.$trackLabel.attr("title",e)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&"sequence"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>10)return fe(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if("all"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const t=this.trackView.track.visibilityWindow;return void 0!==t&&t>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>t}return!0})()){if(this.canvas&&(fe(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const t=this.trackView.minHeight||0;this.setContentHeight(t)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const t=this.referenceFrame;if(this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===t.bpPerPixel){const e=Math.round((this.canvas._data.bpStart-t.start)/t.bpPerPixel);this.canvas.style.left=e+"px"}}setTop(t){if(super.setTop(t),this.canvas){const e=this.$viewport.height(),i=t+this.canvas._data.pixelTop,n=i+this.canvas._data.pixelHeight;(i>0||n0)for(let n of i.roiSets){const i=await n.getFeatures(e,r,s,t.bpPerPixel);o.push({track:n,features:i})}const a=i&&("wig"===i.type||"merged"===i.type);return this.featureCache=new bl(e,r,s,t.bpPerPixel,n,o,a),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}}catch(t){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage("Error loading track data"),this.browser.alert.present(t),console.error(t))}finally{this.loading=!1,this.stopSpinner()}}}repaintDimensions(){const t=ul.isWholeGenomeView(this.referenceFrame.chr),e=t?this.$viewport.width():3*this.$viewport.width(),i=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(t?0:e/3*i),bpEnd:this.referenceFrame.end+(t?0:e/3*i),pixelWidth:e}}repaint(){if(void 0===this.featureCache)return;const{features:t,roiFeatures:e}=this.featureCache,{bpStart:i,bpEnd:n,pixelWidth:r}=this.repaintDimensions(),s=this.$viewport.height(),o=this.getContentHeight(),a=e?Math.max(o,s):o,l=Math.min(a,3*s);if(0===r||0===l)return void(this.canvas&&fe(this.canvas).remove());const h=Math.max(0,-this.contentTop-Math.floor(l/3)),c=this.referenceFrame.bpPerPixel,u=Math.round((i-this.referenceFrame.start)/c),d=(this.contentTop||0)+h,f=document.createElement("canvas");f.style.position="relative",f.style.display="block",f.style.width=r+"px",f.style.height=l+"px",f.style.left=u+"px",f.style.top=d+"px";const p="FILL"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=p*r,f.height=p*l;const g=f.getContext("2d");g.scale(p,p),g.translate(0,-h);const m={context:g,pixelXOffset:u,pixelWidth:r,pixelHeight:l,pixelTop:h,bpStart:i,bpEnd:n,bpPerPixel:c,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(m,t,e),this.canvas&&fe(this.canvas).remove(),f._data=m,this.canvas=f,this.$viewport.append(fe(f))}refresh(){if(!this.canvas||!this.featureCache)return;const t=this.canvas._data;t.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:e,roiFeatures:i}=this.featureCache;this.draw(t,e,i)}draw(t,e,i){if(e&&(t.features=e,this.trackView.track.draw(t)),i&&i.length>0)for(let e of i)t.features=e.features,e.track.draw(t)}containsPosition(t,e){return this.referenceFrame.chr===t&&e>=this.referenceFrame.start&&e<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const t=this.canvas._data,e=t?t.pixelTop:0,i=window.devicePixelRatio,n=this.$viewport.width()*i,r=this.$viewport.height()*i,s=-fe(this.canvas).position().left*i,o=(-this.contentTop-e)*i,a=this.canvas.getContext("2d").getImageData(s,o,n,r),l=document.createElement("canvas"),h=l.getContext("2d");l.width=a.width,l.height=a.height,h.putImageData(a,0,0),Qi((this.$trackLabel.text()?this.$trackLabel.text():"image")+".png",l.toDataURL("image/png"))}saveSVG(){let{width:t,height:e}=this.browser.columnContainer.getBoundingClientRect();const i=new ll({width:t,height:8e3,backdropColor:"white",multiLocusGap:0,viewbox:{x:0,y:0,width:t,height:8e3}});this.renderViewportToSVG(i,{deltaX:32,deltaY:32}),i.setHeight(e);const n=(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,""),r=this.browser.referenceFrameList.indexOf(this.referenceFrame),s=i.getSerializedSvg(!0),o=URL.createObjectURL(new Blob([s],{type:"application/octet-stream"}));Qi(`${n}_referenceFrame_${r}_guid_${_e.guid()}.svg`,o)}renderViewportToSVG(t,{deltaX:e,deltaY:i}){if(this.$zoomInNotice&&this.$zoomInNotice.is(":visible"))return;const{width:n,height:r}=this.$viewport.get(0).getBoundingClientRect(),s=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${_e.guid()}`;this.drawSVGWithContext(t,n,r,s,e,i+this.contentTop,-this.contentTop)}renderSVGContext(t,{deltaX:e,deltaY:i}){if(this.renderViewportToSVG(t,{deltaX:e,deltaY:i}),(!this.$zoomInNotice||!this.$zoomInNotice.is(":visible"))&&this.$trackLabel&&!0===this.browser.trackLabelsVisible){const{x:n,y:r,width:s,height:o}=_e.relativeDOMBBox(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(t,e+n,i+r,s,o)}}renderTrackLabelSVG(t,e,i,n,r){const s=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_track_label_guid_${_e.guid()}`;t.saveWithTranslationAndClipRect(s,e,i,n,r,0),t.fillStyle="white",t.fillRect(0,0,n,r),t.font="12px Arial",t.fillStyle="rgb(68, 68, 68)";const{width:o}=t.measureText(this.$trackLabel.text()),a=.25*(n-o),l=.7*(r-12);t.fillText(this.$trackLabel.text(),a,r-l),t.strokeStyle="rgb(68, 68, 68)",t.strokeRect(0,0,n,r),t.restore()}drawSVGWithContext(t,e,i,n,r,s,o){t.saveWithTranslationAndClipRect(n,r,s,e,i,o);let{start:a,bpPerPixel:l}=this.referenceFrame;const h={context:t,viewport:this,referenceFrame:this.referenceFrame,top:o,pixelTop:o,pixelWidth:e,pixelHeight:i,bpStart:a,bpEnd:a+e*l,bpPerPixel:l,viewportWidth:e,selection:this.selection},c=this.featureCache?this.featureCache.features:void 0,u=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(h,c,u),t.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(t,e,i,n,r){if(this.featureCache&&this.featureCache.containsRange(e,i,n,r))return this.featureCache.features;if("function"==typeof t.getFeatures){const s=await t.getFeatures(e,i,n,r,this);return this.checkContentHeight(s),s}}needsRepaint(){if(!this.canvas)return!0;const t=this.canvas._data;return!t||this.referenceFrame.startt.bpEnd||this.referenceFrame.chr!==t.referenceFrame.chr||this.referenceFrame.bpPerPixel!=t.bpPerPixel}needsReload(){if(!this.featureCache)return!0;const{chr:t,bpPerPixel:e}=this.referenceFrame,{bpStart:i,bpEnd:n}=this.repaintDimensions();return!this.featureCache.containsRange(t,i,n,e)}createZoomInNotice(t){const e=fe("
",{class:"igv-zoom-in-notice-container"});t.append(e);const i=fe("
");return e.append(i),i.text("Zoom in to see features"),e.hide(),e}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const t=this.$viewport.get(0);this.addViewportContextMenuHandler(t);const e=t=>{this.enableClick=!0,this.browser.mouseDownOnViewport(t,this),_e.pageCoordinates(t)};t.addEventListener("mousedown",e),t.addEventListener("touchstart",e);const i=t=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};t.addEventListener("mouseup",i),t.addEventListener("touchend",i),"function"==typeof this.trackView.track.hoverText&&t.addEventListener("mousemove",(t=>{if(0===t.buttons&&Date.now()-gl>100){gl=Date.now();const e=this.createClickState(t);if(e){const t=this.trackView.track.hoverText(e);t?this.$viewport[0].setAttribute("title",t):this.$viewport[0].removeAttribute("title")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&"sequence"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(t){t.addEventListener("contextmenu",(t=>{if(this.browser.dragObject)return!1;const e=this.createClickState(t);if(void 0===e)return!1;t.preventDefault();let i=[];if("function"==typeof this.trackView.track.contextMenuItemList){const t=this.trackView.track.contextMenuItemList(e);t&&(i=t)}i.length>0&&i.push({label:fe("
")}),i.push({label:"Save Image (PNG)",click:()=>this.savePNG()}),i.push({label:"Save Image (SVG)",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(t,i)}))}addViewportClickHandler(t){t.addEventListener("click",(t=>{if(this.enableClick&&this.canvas){if(3===t.which||t.ctrlKey)return;if(fe(".igv-popover").hide(),this.browser.dragObject||this.browser.isScrolling)return;t.preventDefault();const e=_e.translateMouseCoordinates(t,this.$viewport.get(0)).x,i=_e.translateMouseCoordinates(t,this.canvas).x,n=this.referenceFrame,r=Math.floor(n.start+n.toBP(i)),s=Date.now();if(s-plt));t[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=e,i=t.join(" ")}this.browser.search(i)}else this.browser.zoomWithScaleFactor(.5,t,this.referenceFrame)}else t.shiftKey&&"function"==typeof this.trackView.track.shiftClick?this.trackView.track.shiftClick(r,t):"function"==typeof this.trackView.track.popupData&&(fl=setTimeout((()=>{const e=this.getPopupContent(t);e&&(this.popover&&this.popover.dispose(),this.popover=new Oi(this.browser.columnContainer),this.popover.presentContentWithEvent(t,e)),window.clearTimeout(fl),fl=void 0}),this.browser.constants.doubleClickDelay));pl=s}}))}addTrackLabelClickHandler(t){t.addEventListener("click",(t=>{t.stopPropagation();const{track:e}=this.trackView;let i;"function"==typeof e.description?i=e.description():e.description&&(i=`
${e.description}
`),i&&(this.popover&&this.popover.dispose(),this.popover=new Oi(this.browser.columnContainer,e.name||""),this.popover.presentContentWithEvent(t,i))}))}createClickState(t){if(!this.canvas)return;const e=this.referenceFrame,i=_e.translateMouseCoordinates(t,this.$viewport.get(0)),n=_e.translateMouseCoordinates(t,this.canvas),r=e.start+e.toBP(i.x);return{event:t,viewport:this,referenceFrame:e,genomicLocation:r,y:i.y-this.contentTop,canvasX:n.x,canvasY:n.y}}getPopupContent(t){const e=this.createClickState(t);if(void 0===e)return;let i=this.trackView.track;const n=i.popupData(e),r=this.browser.fireEvent("trackclick",[i,n]);let s;return void 0===r||!0===r?n&&n.length>0&&(s=n.map((t=>{if(t.name){const e=`${t.name}   ${t.value}`;return`
${e}
`}return"
"===t?t:t.html?t.html:`
${t}
`})).join("")):"string"==typeof r&&(s=r),s}}class bl{constructor(t,e,i,n,r,s,o){this.chr=t,this.bpStart=e,this.bpEnd=i,this.bpPerPixel=n,this.features=r,this.roiFeatures=s,this.multiresolution=o}containsRange(t,e,i,n){const r=this.multiresolution?this.bpPerPixel/n:1;return e>=this.bpStart&&i<=this.bpEnd&&t===this.chr&&r>.5&&r<2}overlapsRange(t,e,i){return this.chr===t&&i>=this.bpStart&&e<=this.bpEnd}}function yl(t,e){if(!(t.length<6))return{chr:t[0],start:t[1],end:t[2],chr1:t[8],start1:Number.parseInt(t[9]),end1:Number.parseInt(t[10]),chr2:t[13],start2:Number.parseInt(t[14]),end2:Number.parseInt(t[15]),name:t[3],score:Number(t[4]),value:Number(t[5]),color:"."===t[7]?void 0:"0"===t[7]?"rgb(0,0,0)":t[7]};console.log("Skipping line: "+t.join(" "))}const vl=new Set(["transcript","primary_transcript","processed_transcript","mRNA","mrna","lnc_RNA","miRNA","ncRNA","rRNA","scRNA","snRNA","snoRNA","tRNA"]),wl=new Set(["CDS","cds"]),_l=new Set(["start_codon","stop_codon"]),xl=new Set(["5UTR","3UTR","UTR","five_prime_UTR","three_prime_UTR","3'-UTR","5'-UTR"]),kl=new Set(["exon","coding-exon"]),Sl=new Set;for(let _y of[wl,_l,xl,kl])for(let xy of _y)Sl.add(xy);function Cl(t){return t.includes("intron")}function Al(t){return wl.has(t)||_l.has(t)}function Tl(t){return xl.has(t)}function Il(t){return vl.has(t)||t.endsWith("RNA")||t.endsWith("transcript")}function El(t){return Sl.has(t)||t.endsWith("RNA")||Cl(t)}const Ml=new Set(["id","parent","name"]);class Rl{constructor(t){Object.assign(this,t)}popupData(t){const e=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&e.push("
"),this.name&&e.push({name:"Name",value:this.name}),e.push({name:"Type",value:this.type}),e.push({name:"Source",value:this.source}),void 0!==this.score&&e.push({name:"Score",value:this.score}),this.attributeString){const t=Ol(this.attributeString,this.delim);for(let[i,n]of t)void 0!==n&&n.length>0&&!Ml.has(i.toLowerCase())&&e.push({name:i+":",value:n})}return e.push({name:"Location",value:`${this.chr}:${$i(this.start+1)}-${$i(this.end)}`}),e}getAttributeValue(t){if(this.hasOwnProperty(t))return this[t];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(t))return this._attributeCache.get(t);{const e=Ol(this.attributeString,this.delim);let i;for(let[n,r]of e)if(n===t){i=r;break}return this._attributeCache.set(t,i),i}}}class Ll extends Rl{constructor(t){super(t),this.exons=[],this.parts=[]}addExon(t){this.exons.push(t),this.start=Math.min(this.start,t.start),this.end=Math.max(this.end,t.end)}addPart(t){this.parts.push(t)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(t,e){return t.start-e.start}));let t=this.parts[0].start,e=this.parts[0].end;for(let i=1;i=e&&i.start<=t)return i}addCDS(t){let e;const i=this.exons;for(let n of i)if(n.start<=t.start&&n.end>=t.end){e=n;break}e?(e.cdStart=e.cdStart?Math.min(t.start,e.cdStart):t.start,e.cdEnd=e.cdEnd?Math.max(t.end,e.cdEnd):t.end):console.error("No exon found spanning "+t.start+"-"+t.end),this.cdStart=this.cdStart?Math.min(t.start,this.cdStart):t.start,this.cdEnd=this.cdEnd?Math.max(t.end,this.cdEnd):t.end}addUTR(t){let e;const i=this.exons;for(let n=0;n=t.end){e=i[n];break}e?t.start===e.start&&t.end===e.end?e.utr=!0:(t.ende.start&&(e.cdEnd=t.start)):console.error("No exon found spanning "+cds.start+"-"+cds.end)}finish(){this.assembleParts();var t=this.cdStart,e=this.cdEnd;this.exons.sort((function(t,e){return t.start-e.start})),t&&this.exons.forEach((function(i){(i.ende)&&(i.utr=!0)}))}popupData(t){const e=super.popupData(t);for(let i of this.exons)if(!i.pseudo&&t>=i.start&&t");const n=i.popupData(t);for(let t of n)e.push(t)}for(let i of this.parts)if(t>=i.start&&t");const n=i.popupData(t);for(let t of n)e.push(t)}return e}}function Bl(t,e){const i=e.format;if(t.length<9)return;const n="gff3"===i?"=":" ";return new Rl({source:zl(t[1]),type:t[2],chr:t[0],start:parseInt(t[3])-1,end:parseInt(t[4]),score:"."===t[5]?void 0:Number(t[5]),strand:t[6],phase:"."===t[7]?0:parseInt(t[7]),attributeString:t[8],delim:n})}function Nl(t,e){const i=Bl(t,e);if(!i)return;const n=Ol(i.attributeString,i.delim);for(let[t,e]of n){const n=t.toLowerCase();"color"===n||"colour"===n?i.color=xo.createColorString(e):"ID"===t?i.id=e:"Parent"===t&&(i.parent=e)}return i}function Fl(t,e){const i=Bl(t,e);if(!i)return;const n=Ol(i.attributeString,i.delim);let r,s;switch(i.type){case"gene":r="gene_id";break;case"transcript":r="transcript_id",s="gene_id";break;default:s="transcript_id"}for(let[t,e]of n){const n=t.toLowerCase();"color"===n||"colour"===n?i.color=xo.createColorString(e):t===r?i.id=e:t===s&&(i.parent=e)}return i}function Ol(t,e,i=!1){var n=[];for(let r of t.split(";")){r=r.trim();const t=r.indexOf(e);if(t>0&&t2?parseInt(t[2]):n+1;if(isNaN(n)||isNaN(r))return new Ul("Unparsable bed record.");const s=new Jl({chr:i,start:n,end:r,score:1e3});try{if(t.length>3){if(t[3].indexOf(";")>0&&t[3].indexOf("=")>0){const i=Ol(t[3],"=",!0);s.attributes={};for(let t of i)s.attributes[t[0]]=t[1],null!=e.nameField&&t[0]===e.nameField&&(s.name=t[1])}s.name||(s.name="."===t[3]?"":t[3])}if(t.length>4&&(s.score="."===t[4]?0:Number(t[4]),isNaN(s.score)))return s;if(t.length>5&&(s.strand=t[5],"."!==s.strand&&"+"!==s.strand&&"-"!==s.strand))return s;if(t.length>6&&(s.cdStart=parseInt(t[6]),isNaN(s.cdStart)))return s;if(t.length>7&&(s.cdEnd=parseInt(t[7]),isNaN(s.cdEnd)))return s;if(t.length>8&&"."!==t[8]&&"0"!==t[8]&&(s.color=xo.createColorString(t[8])),t.length>11){const e=parseInt(t[9]);if(e>1e3)return s;const i=t[10].replace(/,$/,"").split(","),r=t[11].replace(/,$/,"").split(",");if(i.length!==r.length||e!==i.length)return s;const o=[];for(let t=0;t0&&(Zl(o,s.cdStart,s.cdEnd),s.exons=o)}if(e){let i=e.thicknessColumn,n=e.colorColumn;n&&ni?n.utr=!0:(e>=r&&e<=t&&(n.cdStart=e),i>=r&&i<=t&&(n.cdEnd=i))}}function Yl(t,e){var i,n,r,s,o,a,l;if(!(t.length<9))return i=t[0],n=parseInt(t[1]),r=parseInt(t[2]),o=t[3],a=Number(t[4]),s=t[5].trim(),l=Number(t[6]),0===a&&(a=l),{chr:i,start:n,end:r,name:o,score:a,strand:s,signal:l,pValue:Number(t[7]),qValue:Number(t[8])}}function Ql(t,e){if(t.length<=3)return;const i={chr:t[0],start:parseInt(t[1]),end:parseInt(t[2]),value:Number(t[3])};if(e){let n=e.colorColumn;n&&n0)for(var d=l.split(","),f=0;fu&&(u=m),h.spanning_frag_coords.push({left:g,right:m})}return h.start=c,h.end=u,h}}function ih(t,e){if(t.length<7)return null;const i={chr:t[0],start:parseInt(t[1])-1,end:parseInt(t[2]),"Strongest SNP-risk allele":t[3],"Disease/Phenotype":t[4],"P-value":t[5],"Odds ratio or beta":t[6]};return t.length>6&&(i.PUBMEDID=`${t[7]}`),i}function nh(t,e){const i=e.customFormat;if(t.length1&&(e=t)}else{this.setDecoder(n.format);const t=i.split(this.delimiter||"\t");try{const i=Object.assign({columnNames:e},n);if(this.decode(t,i))break;t.length>1&&(e=t)}catch(i){t.length>1&&(e=t)}}}if(e){n.columnNames=e;for(let t=0;t0&&console.error(`Error parsing line '${s}': ${l.message}`)):l&&e.push(l)}return i===ya&&function(t){if(0==t.length)return;const e=t[0];if(void 0===e.score&&void 0!==e.name){for(let e of t)if(!("number"==typeof(i=e.name)?i-i==0:"string"==typeof i&&""!==i.trim()&&(Number.isFinite?Number.isFinite(+i):isFinite(+i)))&&"."!==e.name)return;for(let e of t)e.score=Number(e.name),delete e.name}var i;const n=t.filter((t=>t.chr1!==t.chr2));for(let e of n){const i=Object.assign({},e);i.dup=!0,t.push(i),e.chr=e.chr1,e.start=e.start1,e.end=e.end1,i.chr=i.chr2,i.start=i.start2,i.end=i.end2}}(e),e}setDecoder(t){switch(t){case"narrowpeak":case"broadpeak":case"regionpeak":case"peaks":this.decode=Yl,this.delimiter=this.config.delimiter||/\s+/;break;case"bedgraph":this.decode=Ql,this.delimiter=/\s+/;break;case"wig":this.decode=Xl,this.delimiter=this.config.delimiter||/\s+/;break;case"gff3":case"gff":this.decode=Nl,this.delimiter="\t";break;case"gtf":this.decode=Fl,this.delimiter="\t";break;case"fusionjuncspan":this.decode=eh,this.delimiter=this.config.delimiter||/\s+/;break;case"gtexgwas":this.skipRows=1,this.decode=ih,this.delimiter="\t";break;case"refflat":this.decode=ql,this.delimiter=this.config.delimiter||/\s+/;break;case"genepred":this.decode=jl,this.delimiter=this.config.delimiter||/\s+/;break;case"genepredext":this.decode=$l,this.delimiter=this.config.delimiter||/\s+/;break;case"ensgene":this.decode=jl,this.header.shift=1,this.delimiter=this.config.delimiter||/\s+/;break;case"refgene":this.decode=$l,this.delimiter=this.config.delimiter||/\s+/,this.header.shift=1;break;case"bed":this.decode=Vl,this.delimiter=this.config.delimiter||/\s+/;break;case"bedpe":case"hiccups":this.decode=ya,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-domain":this.decode=va,this.headerLine=!0,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-loop":this.decode=ya,this.delimiter=this.config.delimiter||"\t",this.header={colorColumn:7};break;case"interact":this.decode=yl,this.delimiter=this.config.delimiter||/\s+/;break;case"snp":this.decode=Kl,this.delimiter="\t";break;case"rmsk":this.decode=Hl,this.delimiter="\t";break;case"gcnv":this.decode=rh,this.delimiter="\t";break;default:const e=xa(t);void 0!==e?(this.decode=nh,this.header.customFormat=e,this.delimiter=e.delimiter||"\t"):(this.decode=Vl,this.delimiter=this.config.delimiter||/\s+/)}}}function oh(t){const e={},i=t.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g);let n;const r=[];for(let t of i)t&&0!==t.trim().length&&(t.endsWith("=")?n=t:n?(r.push(n+t),n=void 0):r.push(t));for(let t of r){if(!t)return;var s=t.split("=",2);if(2===s.length){const t=s[0].trim(),i=s[1].trim();if(e.hasOwnProperty(t)){let n=e[t];Array.isArray(n)?n.push(i):e[t]=[n,i]}else e[t]=i}}return"interact"==e.type?e.format="interact":"gcnv"===e.type&&(e.format="gcnv"),e}function ah(t){let e={},i=t.split(/\s+/);return 2===i.length&&i[1].split(";").forEach((function(t){let i=t.split("=");"color"===i[0]?e.colorColumn=Number.parseInt(i[1])-1:"thickness"===i[0]&&(e.thicknessColumn=Number.parseInt(i[1])-1)})),e}function lh(t){const e=t.split(/\s+/);return{format:"fixedStep",chrom:e[1].split("=")[1],start:parseInt(e[2].split("=")[1],10)-1,step:parseInt(e[3].split("=")[1],10),span:e.length>4?parseInt(e[4].split("=")[1],10):1,index:0}}function hh(t){const e=t.split(/\s+/);return{format:"variableStep",chrom:e[1].split("=")[1],span:e.length>2?parseInt(e[2].split("=")[1],10):1}}class ch{static defaults={height:50,autoHeight:!1,visibilityWindow:void 0,color:void 0,altColor:void 0,supportHiDPI:!0};constructor(t,e){this.browser=e,this.init(t)}init(t){this.config=t,t.displayMode&&(t.displayMode=t.displayMode.toUpperCase());const e=Object.assign({},ch.defaults);if(this.constructor.defaults)for(let t of Object.keys(this.constructor.defaults))e[t]=this.constructor.defaults[t];for(let n of Object.keys(e))this[n]=t.hasOwnProperty(n)?t[n]:e[n],"color"!==n&&"altColor"!==n||(this[n]=ji(i=this[n])&&i.indexOf(",")>0&&!i.startsWith("rgb(")&&!i.startsWith("rgba(")?`rgb(${i})`:i);var i;t.name||t.label?this.name=t.name||t.label:Yi(t.url)?this.name=t.url.name:ji(t.url)&&!t.url.startsWith("data:")&&(this.name=Zi(t.url)),this.url=t.url,this.config.type&&(this.type=this.config.type),this.id=void 0===this.config.id?this.name:this.config.id,this.order=t.order,this.autoscaleGroup=t.autoscaleGroup,this.removable=void 0===t.removable||t.removable,this.minHeight=t.minHeight||Math.min(25,this.height),this.maxHeight=t.maxHeight||Math.max(1e3,this.height),t.onclick&&(this.onclick=t.onclick,t.onclick=void 0),t.description&&("function"==typeof t.description?this.description=t.description:this.description=()=>t.description),t.hoverTextFields?this.hoverText=uh.bind(this):"function"==typeof this.config.hoverText&&(this.hoverText=this.config.hoverText)}get name(){return this._name}set name(t){this._name=t,this.trackView&&this.trackView.setTrackLabelName(t)}updateConfig(t){this.init(t)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}getState(){const t={};for(let i of Object.keys(this.config))i.startsWith("_")||void 0===(e=this.config[i])||"function"==typeof e||e instanceof File||e instanceof Promise||(t[i]=this.config[i]);var e;for(let e of Object.keys(t)){if(e.startsWith("_"))continue;const i=this[e];i&&(aa(i)||"boolean"==typeof i||"metadata"===e)&&(t[e]=i)}const i=ch.defaults;if(this.constructor.defaults)for(let t of Object.keys(this.constructor.defaults))i[t]=this.constructor.defaults[t];for(let e of Object.keys(i))void 0!==this[e]&&i[e]!==this[e]&&(t[e]=this[e]);return!this.autoscale&&this.dataRange&&(t.min=this.dataRange.min,t.max=this.dataRange.max),t}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(t){if(this.disposed)return;const e={};let i;for(let n of Object.keys(t))switch(n.toLowerCase()){case"usescore":e.useScore=1===t[n]||"1"===t[n]||"on"===t[n]||!0===t[n];break;case"visibility":switch(t[n]){case"2":case"3":case"pack":case"full":e.displayMode="EXPANDED";break;case"4":case"squish":e.displayMode="SQUISHED";break;case"1":case"dense":e.displayMode="COLLAPSED"}break;case"color":case"altcolor":e[n]=t[n].startsWith("rgb(")?t[n]:"rgb("+t[n]+")";break;case"featurevisiblitywindow":case"visibilitywindow":e.visibilityWindow=Number.parseInt(t[n]);break;case"maxheightpixels":i=t[n].split(":"),3===i.length&&(e.minHeight=Number.parseInt(i[2]),e.height=Number.parseInt(i[1]),e.maxHeight=Number.parseInt(i[0]));break;case"viewlimits":if(!this.config.autoscale){i=t[n].split(":");let r,s=0;1==i.length?r=Number(i[0]):2==i.length&&(s=Number(i[0]),r=Number(i[1])),e.autoscale=!1,e.dataRange={min:s,max:r},this.viewLimitMin=s,this.viewLimitMax=r}case"name":e[n]=t[n];break;case"url":e.infoURL=t[n];break;case"type":const r=t[n];dh.has(r)?e[n]=dh.get(r):e[n]=r;break;case"graphtype":e.graphType=t[n];break;default:e[n]=t[n]}for(let t of Object.keys(e))if(!this.config.hasOwnProperty(t)||"name"===t&&this.config._derivedName){let i=e[t];if("true"===i&&(i=!0),"false"===i&&(i=!1),this[t]=i,"height"===t&&this.trackView)try{const t=Number.parseInt(i);this.trackView.setTrackHeight(t)}catch(t){console.error(t)}}}clickedFeatures(t){const e=t.viewport.cachedFeatures;if(!e||!Array.isArray(e)||0===e.length)return[];const i=t.genomicLocation,n=t.referenceFrame.bpPerPixel>.2?3*t.referenceFrame.bpPerPixel:.2;return Xo(e,i-n,i+n)}extractPopupData(t,e){const i=new Set(["row","color","chr","start","end","cdStart","cdEnd","strand","alpha"]),n=[];let r,s;for(let e in t)if(t.hasOwnProperty(e)&&!i.has(e)&&aa(t[e])){let i=t[e];n.push({name:Gi(e),value:i}),"alleles"===e?r=t[e]:"alleleFreqs"===e&&(s=t[e])}if(r&&s){r.endsWith(",")&&(r=r.substr(0,r.length-1)),s.endsWith(",")&&(s=s.substr(0,s.length-1));let i=r.split(","),o=s.split(",");if(o.length>1){let r=[];for(let t=0;t=0;i--){let o=r[i].a;if(1===o.length){e||(e=this.getGenomeId());const i=ch.getCravatLink(t.chr,t.start+1,s,o,e);console.log(i),i&&(n.push("
"),n.push({html:i}),n.push("
"))}}}}if(t.attributes)for(let e of Object.keys(t.attributes))n.push({name:e,value:t.attributes[e]});let o=`${t.chr}:${$i(t.start+1)}-${$i(t.end)}`;return t.strand&&(o+=` (${t.strand})`),n.push({name:"Location",value:o}),n}description(){const t=(t,e)=>`
${t}: ${e}
`;let e='
';if(this.url?Yi(this.url)?e+=t("Filename",this.url.name):e+=t("URL",this.url):e=this.name,this.config){if(this.config.metadata)for(let i of Object.keys(this.config.metadata))e+=t(i,this.config.metadata[i]);for(let i of Object.keys(this.config)){if(i.startsWith("_"))continue;let n=i.substr(0,1);if(n!==n.toLowerCase()){const n=this.config[i];n&&aa(n)&&(e+=t(i,n))}}}return e+="
",e}getColorForFeature(t){return"function"==typeof this.color?this.color(feature):this.color}dispose(){this.disposed=!0;for(let t of Object.keys(this))this[t]=void 0}static getCravatLink(t,e,i,n,r){if("hg38"===r||"GRCh38"===r)return`Cravat ${i}->${n}`}}function uh(t){if(!this.hoverTextFields)return;const e=this.clickedFeatures(t);if(e&&e.length>0){let t="";for(let i=0;i0&&(t+="\n"),t="";for(let e of this.hoverTextFields)t.length>0&&(t+="\n"),n.hasOwnProperty(e)?t+=n[e]:"function"==typeof n.getAttribute&&(t+=n.getAttribute(e))}return t}}const dh=new Map([["wiggle_0","wig"],["bed","bed"],["bigBed","bigBed"],["bigWig","bigWig"]]);class fh{constructor(t){switch(this.type=t||"seg",this.type){case"mut":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case"maf":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(t){let e;for(;void 0!==(e=await t.nextLine());)if(!e.startsWith("#")){const t=e.split("\t");this.header={headings:t};break}return this.header}async parseFeatures(t){const e=[];let i;this.header||(this.header=await this.parseHeader(t)),"seg"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(i=this.extractExtraColumns(this.header.headings));const n=this.header.headings[this.dataColumn];let r;for(;void 0!==(r=await t.nextLine());){const t=r.split("\t"),s="seg"===this.type?Number(t[this.dataColumn]):t[this.dataColumn];if(t.length>this.dataColumn){const r=new ph({sample:t[this.sampleColumn],chr:t[this.chrColumn],start:parseInt(t[this.startColumn])-1,end:parseInt(t[this.endColumn]),value:s,valueColumnName:n});if(i){const e=this.extractExtraColumns(t);r.setAttributes({names:i,values:e})}e.push(r)}}return e}extractExtraColumns(t){const e=[];for(let i=0;i=0)return this.attributeValues[e]}}popupData(t,e){const i=new Set(["chr","start","end","sample","value","row","color","sampleKey","uniqueSampleKey","sampleId","chromosome","uniquePatientKey"]),n=this.chr+":"+$i(this.start+1)+"-"+$i(this.end),r=[{name:"Sample",value:this.sample},{name:"Location",value:n},{name:this.valueColumnName?Gi(this.valueColumnName):"Value",value:this.value}];if("mut"===t&&"hg38"===e){const t=this.extractCravatLink(e);t&&(r.push("
"),r.push({html:t}),r.push("
"))}if(this.attributeNames&&this.attributeNames.length>0)for(let t=0;t0)for(let n=0;n"===e||"<*>"===e||"."===e)return"NONVARIANT";{const t=e.split(",").map((function(t){return 1===i&&1===t.length?"SNP":""===t?"NONVARIANT":"OTHER"}));let n=t[0];for(let e of t)if(e!==n)return"MIXED";return n}}(t,e)),"NONVARIANT"===this.type&&(this.heterozygosity=0),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if("NONVARIANT"===this.type)this.start=this.pos-1,this.end=this.start+t.length;else{const i=e.split(",").filter((t=>t.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let e of i)if(this.alleles.push(e),"SV"!==this.type&&yh(e)){let i=e.length,n=t.length;const r=Math.min(i,n);let s=0;for(;s0&&n>0;){const r=s+i-1,o=s+n-1;if(e.charCodeAt(r)!==t.charCodeAt(o))break;i--,n--}for(;i>0&&n>0;){const r=s,o=s;if(e.charCodeAt(r)!==t.charCodeAt(o))break;s++,i--,n--}const o=this.pos+s-1,a=o+n;this.start=void 0===this.start?o:Math.min(this.start,o),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos)}}popupData(t,e){const i=`${$i(this.pos)}`,n=this.start===this.end?`${$i(this.start)} | ${$i(this.start+1)}`:`${$i(this.start+1)}-${$i(this.end)}`,r=[{name:"Chr",value:this.chr},{name:"Pos",value:i},{name:"Loc",value:n},{name:"ID",value:this.names?this.names:""},{name:"Ref",value:this.referenceBases},{name:"Alt",value:this.alternateBases.replace("<","<")},{name:"Qual",value:this.quality},{name:"Filter",value:this.filter}];if("SNP"===this.type){let t=this.referenceBases;if(1===t.length){let i=this.alternateBases.split(",");for(let n of i)if(1===n.length){let i=ch.getCravatLink(this.chr,this.pos,t,n,e);i&&(r.push("
"),r.push({html:i}))}}}if(this.hasOwnProperty("heterozygosity")&&r.push({name:"Heterozygosity",value:this.heterozygosity}),this.info){r.push({html:'
'});for(let t of Object.keys(this.info))r.push({name:t,value:vh(decodeURIComponent(this.info[t]))})}return r}getInfo(t){return this.info?this.info[t]:void 0}isRefBlock(){return"NONVARIANT"===this.type}}const bh=new Set(["A","C","T","G"].map((t=>t.charCodeAt(0))));function yh(t){for(let e=0;e");if(!(e>2&&o>0)){console.log("Malformed VCF header line: "+n);continue}const a=n.substring(2,e-1);i[a]||(i[a]={});const l=Wi(n.substring(e+1,o-1),",");for(let e of l){var r=e.split("=");r.length>1&&("ID"===r[0]?t=r[1]:s[r[0]]=r[1])}t&&(i[a][t]=s)}else if(n.startsWith("##contig")&&e){const t=n.indexOf("",t));const s=n.substring(t+4,r),o=e.getChromosomeName(s);i.chrAliasTable.set(o,s)}}else if(n.startsWith("#CHROM")){const t=n.split("\t");if(t.length>8){i.callSets=[];for(let e=9;e9){const e=_h(t[8].split(":"));n.calls={};for(let r=9;r0?n=t:n?(r.push(n+t),n=void 0):r.push(t));for(let t of r){if(!t)return;var s=t.split("=",2);if(2===s.length){const t=s[0].trim(),i=s[1].trim();e[t]=i}}return e}function Rh(t){let e={},i=t.split(/\s+/);return 2===i.length&&i[1].split(";").forEach((function(t){let i=t.split("=");"color"===i[0]?e.colorColumn=Number.parseInt(i[1])-1:"thickness"===i[0]&&(e.thicknessColumn=Number.parseInt(i[1])-1)})),e}function Lh(t,e){var i,n,r=t.columns;this.aed=t,this.allColumns=e,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=".",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let t=0;t0)for(let t=0;t=0;i--)e=256*e+t[i];else for(let i=0;i0&&(n+=String.fromCharCode(i));return n}getFixedLengthTrimmedString(t){var e,i,n="";for(e=0;e32&&(n+=String.fromCharCode(i));return n}getFloat(){var t=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,t}getDouble(){var t=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,t}skip(t){return this.position+=t,this.position}getVPointer(){var t=this.position,e=this.view.getUint8(t+1)<<8|this.view.getUint8(t),i=4294967296*(255&this.view.getUint8(t+6))+16777216*(255&this.view.getUint8(t+5))+65536*(255&this.view.getUint8(t+4))+256*(255&this.view.getUint8(t+3))+(255&this.view.getUint8(t+2));return this.position+=8,new Fh(i,e)}}class Fh{constructor(t,e){this.block=t,this.offset=e}isLessThan(t){return this.blockt.block||this.block===t.block&&this.offset>t.offset}isEqualTo(t){return this.block===t.block&&this.offset===t.offset}print(){return this.block+":"+this.offset}}function Oh(t,e){if(0===t.length)return t;if(t.sort((function(t,e){const i=t.minv.block-e.minv.block;return 0!==i?i:t.minv.offset-e.minv.offset})),t.length<=1)return t;e&&(t=t.filter((t=>t.maxv.isGreaterThan(e))));const i=[];let n;for(let e of t)n&&Dh(n,e)?e.maxv.isGreaterThan(n.maxv)&&(n.maxv=e.maxv):(i.push(e),n=e);return i}function Dh(t,e){return e.minv.block,t.maxv.block,t.maxv.block-t.minv.block<5e6}class Ph{constructor(t){this.tabix=!0}parse(t,e){const i=new Nh(new DataView(t)),n=i.getInt();if(21582659!==n)throw 38359875===n?Error("CSI version 2 is not supported. Please enter an issue at https://github.com/igvteam/igv.js"):Error("Not a CSI index");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=i.getInt(),this.depth=i.getInt();const r=[];let s=0;if(i.getInt()>=28){i.getInt(),i.getInt(),i.getInt(),i.getInt(),i.getInt(),i.getInt();const t=i.getInt(),n=i.position+t;let s=0;for(;i.positiono)i.getInt(),i.getVPointer(),i.getVPointer(),i.getLong(),i.getLong();else{e[t]=[];const n=i.getInt();for(let r=0;rs&&(s=r.block),e[t].push([n,r]))}}}r>0&&(this.indices[t]={binIndex:e,loffset:n})}this.lastBlockPosition=s}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(t,e,i){const n=this.indices[t];if(n){const t=this.reg2bins(e,i);if(0==t.length)return[];const r=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(n.binIndex[t]){const e=n.binIndex[t];for(let i of e){const e=i[0],n=i[1];r.push({minv:e,maxv:n,bin:t})}}return Oh(r,n.loffset[t[0]])}return[]}reg2bins(t,e){(t-=1)<1&&(t=1),e>2**34&&(e=2**34),e-=1;let i=0,n=0,r=this.minShift+3*this.depth;const s=[];for(;i<=this.depth;r-=3,n+=1<<3*i,i+=1){const i=n+(t>>r),o=n+(e>>r);s.push([i,o])}return s}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}class zh{constructor(){}async parse(t,e,i){const n=[];let r=Number.MAX_SAFE_INTEGER,s=0;const o=new Nh(new DataView(t)),a=o.getInt(),l={};if(!(21578050===a||e&&21578324===a))throw new Error(indexURL+" is not a "+(e?"tabix":"bai")+" file");{const t=o.getInt();if(e){o.getInt(),o.getInt(),o.getInt(),o.getInt(),o.getInt(),o.getInt(),o.getInt();for(let e=0;es&&(s=n.block),t[e].push([i,n]))}}}const l=o.getInt();for(let t=0;t0&&(n[e]={binIndex:t,linearIndex:i})}this.firstBlockPosition=r,this.lastBlockPosition=s,this.indices=n,this.sequenceIndexMap=l,this.tabix=e}}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(t,e,i){const n=this.indices[t];if(n){const t=function(t,e){const i=[];return e>=1<<29&&(e=1<<29),--e,i.push([0,0]),i.push([1+(t>>26),1+(e>>26)]),i.push([9+(t>>23),9+(e>>23)]),i.push([73+(t>>20),73+(e>>20)]),i.push([585+(t>>17),585+(e>>17)]),i.push([4681+(t>>14),4681+(e>>14)]),i}(e,i),r=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(n.binIndex[t]){const e=n.binIndex[t];for(let t of e){const e=t[0],i=t[1];r.push({minv:e,maxv:i})}}const s=n.linearIndex.length;let o;const a=Math.min(e>>14,s-1),l=Math.min(i>>14,s-1);for(let t=a;t<=l;t++){const e=n.linearIndex[t];if(e){o=e;break}}return Oh(r,o)}return[]}}class Uh{constructor(){}async parse(t,e){let i=0;this.chrIndex={},this.lastBlockPosition=[];const n=new Nh(new DataView(t));!function(t){t.getInt(),t.getInt();const e=t.getInt();if(t.getString(),t.getLong(),t.getLong(),t.getString(),t.getInt(),e>=3){let e=t.getInt();for(;e-- >0;)t.getString(),t.getString()}}(n);let r=n.getInt();for(;r-- >0;){let t=n.getString();e&&(t=e.getChromosomeName(t));const r=n.getInt(),s=n.getInt(),o=n.getInt();n.getInt(),n.getInt();let a=n.getLong();const l=[];for(let t=0;ti&&(i=t)}this.chrIndex[t]={chr:t,blocks:l,longestFeature:o,binWidth:r}}this.lastBlockPosition=i}get chromosomeNames(){return Object.keys(this.chrIndex)}chunksForRange(t,e,i){const n=this.chrIndex[t];if(n){const t=n.blocks,r=n.longestFeature,s=n.binWidth,o=Math.max(e-r,0),a=Math.floor(o/s);if(a>=t.length)return[];{const e=Math.min(Math.floor((i-1)/s),t.length-1),n=t[a].min,r=t[e].max;return 0==r-n?[]:[{minv:{block:n,offset:0},maxv:{block:r,offset:0}}]}}}}async function Vh(t,e,i){let n=await zo.loadArrayBuffer(t,la(e)),r=new DataView(n);switch(31===r.getUint8(0)&&139===r.getUint8(1)&&(n=uo(n).buffer,r=new DataView(n)),r.getInt32(0,!0)){case 21578050:return async function(t,e){const i=new zh;return await i.parse(t,!1,e),i}(n,i);case 21578324:return async function(t,e){const i=new zh;return await i.parse(t,!0,e),i}(n,i);case 21582659:return async function(t,e){const i=new Ph;return i.parse(t,e),i}(n,i);case 1480870228:return async function(t,e){const i=new Uh;return i.parse(t,e),i}(n,i);case 38359875:throw Error("CSI version 2 is not supported.");default:throw Error(`Unrecognized index type: ${t}`)}}function Hh(t){return"string"==typeof t||t instanceof String?new jh(t):new $h(t)}class jh{constructor(t){this.data=t,this.ptr=0}nextLine(){var t=this.ptr,e=this.data.indexOf("\n",t),i=this.data;if(e>0)return this.ptr=e+1,e>t&&"\r"===i.charAt(e-1)?i.substring(t,e-1):i.substring(t,e);var n=i.length;return this.ptr=n,t>=n?void 0:i.substring(t)}}class $h{constructor(t){this.data=t,this.length=this.data.length,this.ptr=0}nextLine(){var t,e;if(e="",!(this.ptr>=this.length)){for(var i=this.ptr;i{const e=ArrayBuffer.isView(t)?t:new Uint8Array(t);return 1+(e[17]<<8|e[16])};class Gh{constructor(t){this.config=t,this.cacheBlocks=0!=t.cacheBlocks,this.cache=void 0}async getData(t,e){const i=t.block,n=e.block,r=0===e.offset,s=await this.getInflatedBlocks(i,n,r);if(1===s.length)return s[0];let o=0;for(const t of s)o+=t.byteLength;const a=new Uint8Array(o);let l=0;for(const t of s)a.set(t,l),l+=t.byteLength;return a}async getInflatedBlocks(t,e,i){if(this.cacheBlocks){const n=this.cache;if(n&&n.startBlock<=t&&(n.endBlock>=e||i&&n.nextEndBlock===e)){const i=t-n.startBlock,r=e-n.startBlock;return Yh(n.buffer,i,r)}{let r;if(!n||n.startBlock>e||n.endBlock=n.endBlock)o=n.buffer;else{const i=Math.max(0,t-n.startBlock);let r;if(e>=n.endBlock)r=n.buffer.byteLength;else{const t=Zh(n.buffer);for(let i=0;in.endBlock){const t=await this.loadBLockData(n.endBlock,e,{skipStart:!0,skipEnd:i});s.push(t)}r=function(t){if(1===t.length)return t[0];let e=0;for(const i of t)e+=i.byteLength;const i=new Uint8Array(e);let n=0;for(const e of t)i.set(new Uint8Array(e),n),n+=e.byteLength;return i.buffer}(s)}let s=e;if(i){const t=Zh(r);e=t[t.length-1]}return this.cache={startBlock:t,endBlock:e,nextEndBlock:s,buffer:r},Yh(r)}}return Yh(await this.loadBLockData(t,e,{skipEnd:i}))}async loadBLockData(t,e,i){const n=this.config,r=i&&i.skipStart;let s=0;if(!i||!i.skipEnd){const t=la(n,{range:{start:e,size:26}}),i=await zo.loadArrayBuffer(n.url,t);s=Wh(i)}if(r){const e=la(n,{range:{start:t,size:26}}),i=await zo.loadArrayBuffer(n.url,e);t+=Wh(i)}const o=la(n,{range:{start:t,size:e+s-t}});return zo.loadArrayBuffer(n.url,o)}}function Zh(t){const e=t.byteLength;let i=0;const n=[0];for(;it.blocks)).map((t=>t.max)).reduce(((t,e)=>Math.min(t,e)),Number.MAX_SAFE_INTEGER),n=la(this.config,{bgz:t.tabix,range:{start:0,size:i}});e=Hh(await zo.loadString(this.config.url,n))}return this.header=await this.parser.parseHeader(e),this.header}{const t=la(this.config),e=await zo.loadString(this.config.url,t);let i=Hh(e);return this.header=await this.parser.parseHeader(i),i=Hh(e),this.features=await this.parser.parseFeatures(i),this.header}}getParser(t){switch(t.format){case"vcf":return new wh(t);case"seg":return new fh("seg");case"mut":return new fh("mut");case"maf":return new fh("maf");case"gwas":return new kh(t);case"aed":return new Th(t);default:return new sh(t)}}async loadFeaturesNoIndex(){if(this.features){const t=this.features;return delete this.features,t}{const t=la(this.config),e=await zo.loadString(this.config.url,t);if(!this.header){const t=Hh(e);this.header=await this.parser.parseHeader(t)}const i=Hh(e);return await this.parser.parseFeatures(i)}}async loadFeaturesWithIndex(t,e,i){this.dataURI||this.header||await this.readHeader();const n=this.config,r=this.parser,s=this.index.tabix,o=s?this.index.sequenceIndexMap[t]:t;if(void 0===o)return[];const a=this.genome,l=this.index.chunksForRange(o,e,i);if(l&&0!==l.length){const o=[];for(let h of l){let l;if(s)l=await this._blockLoader.getData(h.minv,h.maxv);else{const t=la(n,{range:{start:h.minv.block,size:h.maxv.block-h.minv.block+1}});l=await zo.loadString(n.url,t)}const c=Hh(h.minv.offset?l.slice(h.minv.offset):l);let u=await r.parseFeatures(c);u=u.filter((t=>void 0===t._f));let d=!1;for(let n=0;ni){o.push(r);break}r.end>=e&&r.start<=i&&(d||(d=!0,n>0&&o.push(u[n-1])),o.push(r))}}return o.sort((function(t,e){return t.start-e.start})),o}return[]}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return Vh(this.config.indexURL,this.config,this.genome)}async loadFeaturesFromDataURI(){if(this.features){const t=this.features;return delete this.features,t}{const t=bo(this.dataURI);let e=Hh(t);return this.header=await this.parser.parseHeader(e),this.header instanceof String&&this.header.startsWith("##gff-version 3")&&(this.format="gff3"),e=Hh(t),this.features=await this.parser.parseFeatures(e),this.features}}}const Xh=ji;class Kh{constructor(t){this.config=t}async readFeatures(t,e,i){let n;n="function"==typeof this.config.url?this.config.url({chr:t,start:e,end:i}):this.config.url.replace("$CHR",t).replace("$START",e).replace("$END",i);let r,s=Object.assign({},this.config);void 0!==this.config.body&&("function"==typeof this.config.body?s.body=this.config.body({chr:t,start:e,end:i}):s.body=this.config.body.replace("$CHR",t).replace("$START",e).replace("$END",i));const o=await zo.load(n,s);if(o&&(r="function"==typeof this.config.parser?this.config.parser(o):Xh(o)?JSON.parse(o):o),this.config.mappings){let t=Object.keys(this.config.mappings);for(let e of r)for(let i of t)e[i]=e[this.config.mappings[i]]}return r}}const Jh=function(t,e){this.config=t,this.genome=e,this.expandQueryInterval=!1};Jh.prototype.readFeatures=function(t,e,i){const n=Math.max(0,Math.floor(e));let r=Math.ceil(i);if(this.genome){const e=this.genome.getChromosome(t);e&&r>e.bpLength&&(r=e.bpLength)}const s=this.config.url+"?db="+this.config.db+"&table="+this.config.tableName+"&chr="+t+"&start="+n+"&end="+r;return zo.loadJson(s,this.config).then((function(t){return t?(t.forEach((function(t){t.hasOwnProperty("exonStarts")&&t.hasOwnProperty("exonEnds")&&t.hasOwnProperty("exonCount")&&t.hasOwnProperty("cdsStart")&&t.hasOwnProperty("cdsEnd")&&function(t){var e,i,n,r,s,o;e=t.exonCount,i=t.exonStarts.split(","),n=t.exonEnds.split(","),r=[];for(var a=0;ao||t.cdsEnd=s&&t.cdsStart<=o&&(l.cdStart=t.cdsStart),t.cdsEnd>=s&&t.cdsEnd<=o&&(l.cdEnd=t.cdsEnd),r.push(l)}t.exons=r}(t)})),t):null}))};const tc=["Name","gene_name","gene","gene_id","alias","locus","name"];class ec{constructor(t){this.format=t.format,this.nameField=t.nameField,this.filterTypes=void 0===t.filterTypes?new Set(["chromosome"]):new Set(t.filterTypes)}combineFeatures(t,e){let i;const n=this.filterTypes;if(t=t.filter((t=>void 0===n||!n.has(t.type))),"gff3"===this.format){const e=this.combineFeaturesById(t);i=this.combineFeaturesByType(e)}else i=this.combineFeaturesByType(t);return i.sort((function(t,e){return t.start-e.start})),this.numberExons(i,e),this.nameFeatures(i),i}combineFeaturesById(t){const e=new Map,i=[];for(let n of t)if(El(n.type)||Il(n.type)||!n.id)i.push(n);else{let t=e.get(n.chr);t||(t=new Map,e.set(n.chr,t));let i=t.get(n.id);i?i.push(n):t.set(n.id,[n])}for(let t of e.values())for(let e of t.values())if(e.length>1){const t=e[0];t.exons=[];for(let i of e)t.start=Math.min(t.start,i.start),t.end=Math.max(t.end,i.end),t.exons.push({start:i.start,end:i.end});i.push(t)}else i.push(e[0]);return i}combineFeaturesByType(t){const e=t.filter((t=>"gene"===t.type||t.type.endsWith("_gene"))),i=Object.create(null);for(let t of e)i[t.id]=t;const n=Object.create(null),r=[],s=new Set,o=this.filterTypes;t=t.filter((t=>void 0===o||!o.has(t.type)));for(let e of t)if("biological_region"===e.type&&console.log(),Il(e.type)){const t=e.id;if(void 0!==t){const o=new Ll(e);n[t]=o,r.push(o),s.add(e);const a=i[e.parent];a&&(o.geneObject=a,s.add(a))}}for(let e of t)if(El(e.type)){const t=h(e);if(t)for(let i of t){let o=n[i];if(!o&&"gtf"===this.format){const t=Object.assign({},e);t.type="transcript",o=new Ll(t),n[i]=o,r.push(o)}if(void 0!==o){if(a=e.type,kl.has(a))if(t.length>1){const t=new Rl(e);o.addExon(t)}else o.addExon(e);else o.addPart(e);s.add(e)}}}var a;r.forEach((function(t){"function"==typeof t.finish&&t.finish()}));const l=t.filter((t=>!s.has(t)));for(let t of l)r.push(t);return r;function h(t){return t.parent&&""!==t.parent.trim()?t.parent.trim().split(","):null}}numberExons(t,e){for(let i of t)if(i.exons&&(!e||i.end<=e.end&&i.start>e.start))for(let t=0;t0){const t=1===this.variant_types.length?"Type":"Types";let i;for(let t of this.variant_types)i?i+=", "+t.display_name:i=t.display_name;e.push({name:t,value:i})}return e.push({name:"Actionability",value:this.actionabilityScore}),e.push({name:"Location",value:this.locationString}),e;function i(t,e){return""+t+""}}}class cc{constructor(t,e){if(this.config=t,this.genome=e,this.format=t.format?t.format.toUpperCase():"BAM","BAM"!==this.format&&"VCF"!==this.format)throw Error(`htsget format ${t.format} is not supported`)}async readHeaderData(){const t=`${uc(this.config)}?class=header&format=${this.format}`,e=await zo.loadJson(t,la(this.config));return await this.loadUrls(e.htsget.urls)}async readData(t,e,i){const n=`${uc(this.config)}?format=${this.format}&referenceName=${t}&start=${Math.floor(e)}&end=${Math.ceil(i)}`,r=await zo.loadJson(n,la(this.config));return this.loadUrls(r.htsget.urls)}async loadUrls(t){const e=[];for(let i of t)if(i.url.startsWith("data:"))e.push(Promise.resolve(dc(i.url)));else{const t=la(this.config||{});i.headers&&(t.headers=Object.assign(t.headers||{},i.headers)),e.push(zo.loadArrayBuffer(i.url,t))}return function(t){let e=0;for(let i of t)e+=i.byteLength;let i=0;const n=new Uint8Array(e);for(let e of t){const t=new Uint8Array(e);n.set(t,i),i+=t.length}return n}(await Promise.all(e))}static async inferFormat(t){try{const e=uc(t),i=`${e}${e.includes("?")?"&":"?"}class=header`,n=await zo.loadJson(i,la(t));if(n.htsget){const e=n.htsget.format;if("BAM"!==e&&"VCF"!==e)throw Error(`htsget format ${e} is not supported`);t.format=e.toLowerCase(),t.sourceType="htsget",t.name||(t.name=await ua(t.url))}}catch(t){}}}function uc(t){if(t.url&&t.endpoint&&t.id)return t.url+t.endpoint+t.id;if(t.endpoint&&t.id)return t.endpoint+t.id;if(t.url)return t.url.startsWith("htsget://")?t.url.replace("htsget://","https://"):t.url;throw Error("Must specify either 'url', or 'endpoint' and 'id")}function dc(t){const e=t.split(","),i=e[0].split(":")[1];let n=e[1];n=i.indexOf("base64")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s=i[t]){n.row=t,i[t]=n.end;break}n.row=t,i[t]=n.end}}function gc(t,e,i){const n=i||1e4,r=t=>{const i=Object.assign({},t);return i.chr="all",i.start=e.getGenomeCoordinate(t.chr,t.start),i.end=e.getGenomeCoordinate(t.chr,t.end),i._f=t,i.exons&&delete i.exons,i},s=new Set(e.wgChromosomeNames),o=[];let a=0;for(let i of e.wgChromosomeNames){if(Array.isArray(t)){const i={};for(let n of t){const t=e.getChromosomeName(n.chr);i.hasOwnProperty(t)||(i[t]=[]),i[t].push(n)}t=i}const l=t[i];if(l)for(let t of l){let i=e.getChromosomeName(t.chr);if(s.has(i))if(o.lengthi-e&&!1!==this.config.expandQuery){const t=Math.min(4.1*(i-e),n);s=Math.max(0,(e+i)/2-t),o=e+t}let a=await r.readFeatures(t,s,o);void 0===this.queryable&&(this.queryable=r.indexed);const l=this.queryable?new Da(t,s,o):void 0;a?(!1===this.config.assembleGFF||"gtf"!==this.config.format&&"gff3"!==this.config.format&&"gff"!==this.config.format||(a=new ec(this.config).combineFeatures(a,l)),"wig"!==this.config.format&&"junctions"!==this.config.type&&mc(a,this.config.maxRows||Number.MAX_SAFE_INTEGER),this.featureCache=new Zo(a,this.genome,l),this.searchable&&this.genome.addFeaturesToDB(a,this.config)):this.featureCache=new Zo([],l)}}class yc{constructor(t,e,i){this.path=t.url,this.bufferSize=i||512e3,this.range={start:-1,size:-1},this.config=t}async dataViewForRange(t,e,i=0){try{if(!(this.data&&this.range.start<=t.start&&this.range.start+this.range.size>=t.start+t.size)){let e;e=t.size?Math.max(this.bufferSize,t.size):this.bufferSize,this.contentLength&&(e=Math.min(e,this.contentLength-t.start));const i={start:t.start,size:e},n=await zo.loadArrayBuffer(this.path,la(this.config,{range:i}));this.data=n,this.range=i}const i=this.data.byteLength,n=t.start-this.range.start;return e?new Uint8Array(this.data,n,i-n):new DataView(this.data,n,i-n)}catch(n){if(0===i&&n.message&&n.message.startsWith("416")){try{return this.contentLength=await zo.getContentLength(this.path,la(this.config)),this.dataViewForRange(t,e,++i)}catch(t){console.error(t)}throw n}}}}let vc=512e3;class wc{constructor(t,e){this.path=t.url,this.format=t.format||"bigwig",this.genome=e,this.rpTreeCache={},this.config=t,this.loader=fa(this.path)?new Rc(this.path):zo}async readWGFeatures(t,e){await this.loadHeader();const i=this.chromTree.idToChrom.length-1,n=this.chromTree.idToChrom[0],r=this.chromTree.idToChrom[i];return this.readFeatures(n,0,r,Number.MAX_VALUE,t,e)}async readFeatures(t,e,i,n,r,s){await this.loadHeader();const o=this.chromTree.chromToID[t],a=this.chromTree.chromToID[i];if(void 0===o||void 0===a)return[];let l,h;if("bigwig"===this.type){const t=await this.getZoomHeaders();let e=r?function(t,e){let i;for(let n=0;n0?lo(r):r,h.call(this,new DataView(u.buffer),o,e,a,n,c,this.chromTree.idToChrom,s)}return c.sort((function(t,e){return t.start-e.start})),c}return[]}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let t,e=await this.loader.loadArrayBuffer(this.path,la(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;let i=new Nh(new DataView(e)),n=i.getUInt();if(2291137574===n)this.type="bigwig";else if(2273964779===n)this.type="bigbed";else{this.littleEndian=!1,i.littleEndian=!1,i.position=0;let t=i.getUInt();654085990===t?this.type="bigwig":3958540679===t&&(this.type="bigbed")}t={bwVersion:i.getUShort(),nZoomLevels:i.getUShort(),chromTreeOffset:i.getLong(),fullDataOffset:i.getLong(),fullIndexOffset:i.getLong(),fieldCount:i.getUShort(),definedFieldCount:i.getUShort(),autoSqlOffset:i.getLong(),totalSummaryOffset:i.getLong(),uncompressBuffSize:i.getInt(),extensionOffset:i.getLong()};const r=64;let s={start:r,size:t.fullDataOffset-r+5};e=await this.loader.loadArrayBuffer(this.path,la(this.config,{range:s}));const o=t.nZoomLevels;i=new Nh(new DataView(e)),this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let t=1;t<=o;t++){const e=o-t,n=new _c(e,i);this.firstZoomDataOffset=Math.min(n.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[e]=n}if(t.autoSqlOffset>0){i.position=t.autoSqlOffset-r;const e=i.getString();e&&(this.autoSql=function(t){let e;const i=[];let n=!1;const r=t.trim().split(/\s*[\r\n]+\s*/g);for(let t of r)if(t.startsWith("table"))e=t.split(/\s+/)[1].trim();else if(t.startsWith("("))n=!0;else if(t.startsWith(")"));else if(n&&t.length>0){const e=t.indexOf(";"),n=t.substr(0,e).split(/\s+/),r=t.substr(e+1).replace(/"/g,"").trim();i.push({type:n[0],name:n[1],description:r})}return{table:e,fields:i}}(e))}if(t.totalSummaryOffset>0&&(i.position=t.totalSummaryOffset-r,this.totalSummary=new Ac(i)),!(t.chromTreeOffset>0))throw"BigWig chromosome tree offset <= 0";return i.position=t.chromTreeOffset-r,this.chromTree=new Sc(i,r,this.genome),i.position=t.fullDataOffset-r,t.dataCount=i.getInt(),this.setDefaultVisibilityWindow(t),this.header=t,this.header}}async loadRPTree(t){let e=this.rpTreeCache[t];return e||(e=new xc(t,this.config,this.littleEndian,this.loader),await e.load(),this.rpTreeCache[t]=e,e)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),"bigwig"===this.type?"wig":this.autoSql&&"chromatinInteract"===this.autoSql.table?"interact":"annotation"}setDefaultVisibilityWindow(t){if("bigwig"===this.type)this.visibilityWindow=-1;else{let e=this.genome?this.genome.getGenomeLength():3088286401;this.visibilityWindow=t.dataCount<1e3?-1:e/t.dataCount*1e3}}}class _c{constructor(t,e){this.index=t,this.reductionLevel=e.getInt(),this.reserved=e.getInt(),this.dataOffset=e.getLong(),this.indexOffset=e.getLong()}}class xc{constructor(t,e,i,n){this.config=e,this.loader=n,this.fileOffset=t,this.path=e.url,this.littleEndian=i}async load(){const t=this.fileOffset+48,e=fa(this.path)?this.loader:new yc(this.config,vc);return this.rootNode=await this.readNode(t,e),this}async readNode(t,e){let i=await e.dataViewForRange({start:t,size:4},!1),n=new Nh(i,this.littleEndian);const r=1===n.getByte();n.getByte();const s=n.getUShort();let o={start:t+=4,size:s*(r?32:24)};i=await e.dataViewForRange(o,!1);const a=new Array(s);if(n=new Nh(i),r){for(let t=0;t=0&&(n.position=r);let o=n.getByte();n.getByte();let a,l,u,d,f,p,g=n.getUShort();if(1===o)for(a=0;at.startChrom||n===t.startChrom&&r>=t.startBase)&&(e0){this.mean=this.sumData/t,this.stddev=Math.sqrt(this.sumSquares/(t-1));let e=this.minVal<0?this.mean-2*this.stddev:0,i=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:e,max:i}}}function Ic(t,e,i,n,r,s,o){const a=new Nh(t),l=a.getInt(),h=a.getInt();let c=h,u=a.getInt();const d=a.getInt(),f=a.getInt(),p=a.getByte();a.getByte();let g=a.getUShort();if(l>=e&&l<=n){let t=0;for(;g-- >0;){let g;switch(p){case 1:c=a.getInt(),u=a.getInt(),g=a.getFloat();break;case 2:c=a.getInt(),g=a.getFloat(),u=c+f;break;case 3:g=a.getFloat(),c=h+t*d,u=c+f,t++}if(!(ln||l===n&&c>=r)break;if(Number.isFinite(g)){const t=o[l];s.push({chr:t,start:c,end:u,value:g})}}}}}function Ec(){const t=function(t,e,i,n){if("biginteract"===n||i&&"chromatinInteract"===i.table||"interact"===i.table)return function(t,e){return t.chr1=e[5],t.start1=Number.parseInt(e[6]),t.end1=Number.parseInt(e[7]),t.chr2=e[10],t.start2=Number.parseInt(e[11]),t.end2=Number.parseInt(e[12]),t.name=e[0],t.score=Number(e[1]),t.value=Number(e[2]),t.color="."===e[4]?void 0:"0"===e[4]?"rgb(0,0,0)":e[4],t};{const n=t-3;return function(r,s){if(n>0&&(r.name=s[0]),n>1&&(r.score=Number(s[1])),n>2&&(r.strand=s[2]),n>3&&(r.cdStart=parseInt(s[3])),n>4&&(r.cdEnd=parseInt(s[4])),n>5&&"."!==s[5]&&"0"!==s[5]&&"-1"!==s[5]){const t=xo.createColorString(s[5]);r.color=t.startsWith("rgb")?t:void 0}if(n>8){const t=parseInt(s[6]),e=s[7].split(","),i=s[8].split(","),n=[];for(let s=0;si?n.utr=!0:(e>=r&&e<=t&&(n.cdStart=e),i>=r&&i<=t&&(n.cdEnd=i))}}(n,r.cdStart,r.cdEnd),r.exons=n}if(i)for(let n=t;n=13;){const e=l.getInt(),h=a[e],c=l.getInt(),u=l.getInt(),d=l.getString();if(!(er||e===r&&c>=s)break;if(u>0){const e={chr:h,start:c,end:u};o.push(e);const i=d.split("\t");t(e,i)}}}}}function Mc(t,e,i,n,r,s,o,a){const l=new Nh(t);for(;l.remLength()>=32;){const t=l.getInt(),h=o[t],c=l.getInt(),u=l.getInt(),d=l.getInt(),f=l.getFloat(),p=l.getFloat(),g=l.getFloat();let m;switch(l.getFloat(),a){case"min":m=f;break;case"max":m=p;break;default:m=0===d?0:g/d}if(!(tn||t===n&&c>=r)break;Number.isFinite(m)&&s.push({chr:h,start:c,end:u,value:m})}}}class Rc{constructor(t){this.data=bo(t).buffer}loadArrayBuffer(t,e){const i=e.range;return i?this.data.slice(i.start,i.start+i.size):this.data}async dataViewForRange(t,e){const i=Math.min(this.data.byteLength-t.start,t.size);return e?new Uint8Array(this.data,t.start,i):new DataView(this.data,t.start,i)}}class Lc{constructor(t,e){this.reader=new wc(t,e),this.genome=e,this.format=t.format||"bigwig",this.wgValues={},this.queryable=!0}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n,windowFunction:r}){const s="bigwig"===this.reader.type,o="all"===t.toLowerCase()?s?await this.getWGValues(r):[]:await this.reader.readFeatures(t,e,t,i,n,r);return s||pc(o),o}async getHeader(){return this.reader.loadHeader()}getDefaultRange(){return void 0!==this.reader.totalSummary?this.reader.totalSummary.defaultRange:void 0}async defaultVisibilityWindow(){return this.reader.defaultVisibilityWindow}async getWGValues(t){const e=this.genome;if(this.wgValues[t])return this.wgValues[t];{const i=e.getGenomeLength()/1e3,n=await this.reader.readWGFeatures(i,t);let r=[];for(let t of n){const i=t.chr,n=e.getCumulativeOffset(i),s=Object.assign({},t);s.chr="all",s.start=n+t.start,s.end=n+t.end,r.push(s)}return this.wgValues[t]=r,r}}supportsWholeGenome(){return"bigwig"===this.reader.type}async trackType(){return this.reader.getTrackType()}}class Bc{constructor(t,e){this.config=t,this.genome=e,this.path=t.url,this.groupCache={},this.datasetCache={}}async readHeader(){if(void 0!==this.magic)return this;let t=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:0,size:64e3}})),e=new Nh(new DataView(t));if(this.magic=e.getInt(),this.version=e.getInt(),this.indexPos=e.getLong(),this.indexSize=e.getInt(),e.getInt(),this.version>=2){let t=e.getInt();for(this.windowFunctions=[];t-- >0;)this.windowFunctions.push(e.getString())}this.trackType=e.getString(),this.trackLine=e.getString();let i=e.getInt();for(this.trackNames=[];i-- >0;)this.trackNames.push(e.getString());this.genomeID=e.getString(),this.flags=e.getInt(),this.compressed=0!=(1&this.flags),t=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:this.indexPos,size:this.indexSize}})),e=new Nh(new DataView(t)),this.datasetIndex={};let n=e.getInt();for(;n-- >0;){const t=e.getString(),i=e.getLong(),n=e.getInt();this.datasetIndex[t]={position:i,size:n}}for(this.groupIndex={},n=e.getInt();n-- >0;){const t=e.getString(),i=e.getLong(),n=e.getInt();this.groupIndex[t]={position:i,size:n}}return this}async readDataset(t,e,i){const n=t+"_"+e+"_"+i;if(this.datasetCache[n])return this.datasetCache[n];{await this.readHeader();const r=this.version<2?"":"/"+e,s="all"===t.toLowerCase()||void 0===i?"0":i.toString();let o;o="raw"===e?"/"+t+"/raw":"/"+t+"/z"+s+r;const a=this.datasetIndex[o];if(void 0===a)return;const l=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:a.position,size:a.size}}));if(!l)return;const h=new Nh(new DataView(l));let c=h.getInt();const u={};for(;c-- >0;)u[h.getString()]=h.getString();const d=h.getString(),f=h.getFloat();let p=h.getInt();const g=[];for(;p-- >0;)g.push({position:h.getLong(),size:h.getInt()});const m={name:o,attributes:u,dataType:d,tileWidth:f,tiles:g};return this.datasetCache[n]=m,m}}async readRootGroup(){const t=this.genome,e=this.groupCache["/"];if(e)return e;{const e=await this.readGroup("/"),i=e.chromosomes,n=e.maxZoom;n&&(this.maxZoom=Number(n));const r=e.totalCount;r&&(e.totalCount=Number(r));const s={};return i&&i.split(",").forEach((function(e){const i=t.getChromosomeName(e);s[i]=e})),this.chrAliasTable=s,this.groupCache["/"]=e,e}}async readGroup(t){const e=this.groupCache[t];if(e)return e;{await this.readHeader();const e=this.groupIndex[t];if(void 0===e)return;const i=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:e.position,size:e.size}}));if(!i)return;const n=new Nh(new DataView(i)),r={name:t};let s=n.getInt();for(;s-- >0;){const t=n.getString(),e=n.getString();r[t]=e}return this.groupCache[t]=r,r}}async readTiles(t,e){if(t.sort((function(t,e){return t.position-e.position})),0===(t=t.filter((function(t){return t.size>0}))).length)return Promise.resolve([]);const i=t[0],n=t[t.length-1],r=i.position,s=n.position+n.size-r,o=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:r,size:s}})),a=[];for(let i of t){const t=i.position-r,n=i.size;if(n>0){let i;i=this.compressed?lo(o.slice(t,t+n)).buffer:o.slice(t,t+n);const r=new Nh(new DataView(i)),s=r.getString();let l;switch(s){case"fixedStep":l=Nc(r,e);break;case"variableStep":l=Fc(r,e);break;case"bed":case"bedWithName":l=Oc(r,e,s);break;default:throw"Unknown tile type: "+s}a.push(l)}}return a}async readTile(t,e){let i=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:t.position,size:t.size}}));this.compressed&&(i=lo(i).buffer);const n=new Nh(new DataView(i)),r=n.getString();switch(r){case"fixedStep":return Nc(n,e);case"variableStep":return Fc(n,e);case"bed":case"bedWithName":return Oc(n,e,r);default:throw"Unknown tile type: "+r}}}function Nc(t,e){const i=t.getInt(),n=t.getInt(),r=t.getFloat(),s=[];let o=e;for(;o-- >0;){let e=i;const n=[];for(;e-- >0;)n.push(t.getFloat());s.push(n)}return{type:"fixedStep",start:n,span:r,data:s,nTracks:e,nPositions:i}}function Fc(t,e){const i=t.getInt(),n=t.getFloat(),r=t.getInt(),s=[];let o=r;for(;o-- >0;)s.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){o=r;const e=[];for(;o-- >0;)e.push(t.getFloat());a.push(e)}return{type:"variableStep",tileStart:i,span:n,start:s,data:a,nTracks:e,nPositions:r}}function Oc(t,e,i){const n=t.getInt();let r=n;const s=[];for(;r-- >0;)s.push(t.getInt());r=n;const o=[];for(;r-- >0;)o.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){let e=n;const i=[];for(;e-- >0;)i.push(t.getFloat());a.push(i)}if("bedWithName"===i){r=n;const e=[];for(;r-- >0;)e.push(t.getString())}return{type:i,start:s,end:o,data:a,nTracks:e,nPositions:n}}class Dc{constructor(t,e){this.genome=e,this.windowFunction=t.windowFunction||"mean",this.reader=new Bc(t,e),this.queryable=!0}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n}){if("all"===t.toLowerCase()){const t=[],e=this.genome;if(this.genome.wgChromosomeNames)for(let i of e.wgChromosomeNames){const r=e.getChromosome(i).bpLength;n=r/1e3;const s=await this._getFeatures(i,0,r,n);if(s)for(let i of s){const n=Object.assign({},i);n.chr="all",n.start=e.getGenomeCoordinate(i.chr,i.start),n.end=e.getGenomeCoordinate(i.chr,i.end),n._f=i,t.push(n)}}return t}return this._getFeatures(t,e,i,n)}async _getFeatures(t,e,i,n){const r=new Da(t,e,i),s=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const t=this.rootGroup.totalCount;t&&(this.normalizationFactor=1e6/t)}r.bpPerPixel=n;const o=function(t,e,i){var n=i.getChromosome(t).bpLength;return Math.ceil(Math.log(Math.max(0,n/(700*e)))/Vc)}(t,n,s);let a=this.reader.chrAliasTable[t],l=this.reader.maxZoom;void 0===a&&(a=t),void 0===l&&(l=-1);const h=o>l?"raw":this.windowFunction,c=await this.reader.readDataset(a,h,o);if(null==c)return[];const u=c.tileWidth,d=Math.floor(e/u),f=Math.floor(i/u),p=await this.reader.readTiles(c.tiles.slice(d,f+1),1),g=[];for(let n of p)switch(n.type){case"bed":Pc(n,t,e,i,0,g);break;case"variableStep":zc(n,t,e,i,0,g);break;case"fixedStep":Uc(n,t,e,i,0,g);break;default:throw"Unknown tile type: "+n.type}return g.sort((function(t,e){return t.start-e.start})),g}get supportsWholeGenome(){return!0}}function Pc(t,e,i,n,r,s){const o=t.nPositions,a=t.start,l=t.end,h=t.data[0];for(let t=0;tn)break;s.push({chr:e,start:r,end:o,value:h[t]})}}}function zc(t,e,i,n,r,s){const o=t.nPositions,a=t.start,l=t.span,h=t.data[0];for(let t=0;tn)break;s.push({chr:e,start:r,end:o,value:h[t]})}}}function Uc(t,e,i,n,r,s){const o=t.nPositions;let a=t.start;const l=t.span,h=t.data[0];for(let t=0;tn)break;r>=i&&(Number.isNaN(h[t])||s.push({chr:e,start:a,end:r,value:h[t]})),a=r}}var Vc=Math.log(2);class Hc{constructor(t,e){this.config=t,this.genome=e,this.queryable=!1,this.searchable=!1!==t.searchable,this.updateFeatures(t.features)}updateFeatures(t){mc(t=function(t,e){if(e)for(let i of t)i.chr=e.getChromosomeName(i.chr);return t}(t,this.genome)),this.config.mappings&&function(t,e){let i=Object.keys(e);t.forEach((function(t){i.forEach((function(i){t[i]=t[e[i]]}))}))}(t,this.config.mappings),this.featureCache=new Zo(t,this.genome),(this.searchable||this.config.searchableFields)&&this.genome.addFeaturesToDB(t,this.config)}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome,o=s?s.getChromosomeName(t):t;return"all"===o.toLowerCase()?gc(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(o,e,i)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}}const jc=new Set(["bigwig","bw","bigbed","bb","biginteract","biggenepred","bignarrowpeak"]);function $c(t,e){const i=t.format?t.format.toLowerCase():void 0;return t.features?new Hc(t,e):jc.has(i)?new Lc(t,e):"tdf"===i?new Dc(t,e):new bc(t,e)}const qc=function(t,e){const{r:i,g:n,b:r}=Ko.nickel;return`rgba(${i},${n},${r},0.125)`}(),Wc=qc;class Gc{constructor(t,e){if(this.url=t.url,t.name?this.name=t.name:t.url&&Yi(t.url)?this.name=t.url.name:t.url&&ji(t.url)&&!t.url.startsWith("data:")&&(this.name=Zi(t.url)),this.isUserDefined=t.isUserDefined,t.features)this.featureSource=new Yc(t.features,e);else{if(t.format)t.format=t.format.toLowerCase();else{const e=Zi(t.url);t.format=ka(e)}this.featureSource=t.featureSource||$c(t,e)}!0===this.isUserDefined?(this.color=t.color||Wc,this.headerColor="rgba(155,185,129)"):(this.color=t.color||qc,this.headerColor="rgb(190,190,190)")}async getFeatures(t,e,i){return this.featureSource.getFeatures({chr:t,start:e,end:i})}async getAllFeatures(){return"function"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(t){this.isUserDefined?this.featureSource.addFeature(t):console.error("Attempt to add ROI to non user-defined set")}removeFeature(t){this.isUserDefined?this.featureSource.removeFeature(t):console.error("Attempt to remove ROI from non user-defined set")}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined};{const t=this.featureSource.getAllFeatures(),e=[];for(let i of Object.keys(t))for(let n of t[i])e.push(n);return{name:this.name,color:this.color,features:e,isUserDefined:this.isUserDefined}}}dispose(){for(let t of Object.keys(this))this[t]=void 0}}function Zc(t,e,i,n){let r=Math.round((t-i)/n),s=Math.round((e-i)/n)-r;return s<3&&(s=3,r-=1),{x:r,width:s}}class Yc{constructor(t,e){this.featureMap={},this.genome=e;for(let i of t){const t=e?e.getChromosomeName(i.chr):i.chr;let n=this.featureMap[t];n||(n=[],this.featureMap[t]=n),n.push(i)}for(let t of Object.keys(this.featureMap))this.featureMap[t].sort(((t,e)=>t.start-e.start))}getFeatures({chr:t,start:e,end:i}){if("all"===t.toLowerCase())return gc(this.featureMap,this.genome);{const n=this.featureMap[t];return n?n.filter((t=>t.end>e&&t.startt.start-e.start))}removeFeature({chr:t,start:e,end:i}){if(this.featureMap[t]){const n=`${t}-${e}-${i}`;this.featureMap[t]=this.featureMap[t].filter((t=>n!==`${t.chr}-${t.start}-${t.end}`))}}}class Qc{constructor(t,e,i,n){this.rulerViewport=t,this.rulerSweeper=_e.div({class:"igv-ruler-sweeper"}),e.appendChild(this.rulerSweeper),this.browser=i,this.referenceFrame=n,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(ul.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on("locuschange",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off("locuschange",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let t,e,i,n,r,s;this.boundContentMouseDownHandler=function(s){t=!0,e=!0;const{x:o}=_e.translateMouseCoordinates(s,this.rulerViewport.contentDiv);n=i=o,r=1,this.rulerSweeper.style.display="block",this.rulerSweeper.style.backgroundColor=!0===s.shiftKey?Wc:"rgba(68, 134, 247, 0.25)",this.rulerSweeper.style.left=`${n}px`,this.rulerSweeper.style.width=`${r}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener("mousedown",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(o){let a;if(t&&e){const{x:t}=_e.translateMouseCoordinates(o,this.rulerViewport.contentDiv);a=Math.max(Math.min(t,this.rulerViewport.contentDiv.clientWidth),0),s=a-i,r=Math.abs(s),this.rulerSweeper.style.width=`${r}px`,s<0&&(n=i+s,this.rulerSweeper.style.left=`${n}px`)}}.bind(this),document.addEventListener("mousemove",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(i){let s;!0===t&&!0===e&&(t=e=void 0,this.rulerSweeper.style.display="none",r>1)&&(s={start:Math.floor(this.referenceFrame.calculateEnd(n)),end:Math.floor(this.referenceFrame.calculateEnd(n+r))},!0===i.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},s)):(ca(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,s,this.browser.minimumBases()),function(t,e,i){t.start=Math.round(e.start),t.end=Math.round(e.end),t.bpPerPixel=(t.end-t.start)/i}(this.referenceFrame,s,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame)))}.bind(this),document.addEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener("mousedown",this.boundContentMouseDownHandler),document.removeEventListener("mousemove",this.boundDocumentMouseMoveHandler),document.removeEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}class Xc{constructor(t){this.paired=!0,this.firstAlignment=t,this.chr=t.chr,this.readName=t.readName,t.starte.start?this.connectingEnd=t.start:this.connectingStart=t.start+t.lengthOnRef,this.start=Math.min(e.start,t.start),this.end=Math.max(e.start+e.lengthOnRef,t.start+t.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(e.scStart,t.scStart);const i=Math.max(e.scStart+e.scLengthOnRef,t.scStart+t.scLengthOnRef);this.scLengthOnRef=i-this.scStart}containsLocation(t,e){const i=e?this.scStart:this.start,n=e?this.scLengthOnRef:this.lengthOnRef;return t>=i&&t<=i+n}alignmentContaining(t,e){return this.firstAlignment.containsLocation(t,e)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(t,e)?this.secondAlignment:void 0}popupData(t){let e=this.firstAlignment.popupData(t);return this.secondAlignment&&(e.push("-------------------------------"),e=e.concat(this.secondAlignment.popupData(t))),e}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}firstOfPairStrand(){return this.firstAlignment.isFirstOfPair()?this.firstAlignment.strand:this.secondAlignment&&this.secondAlignment.isFirstOfPair()?this.secondAlignment.strand:this.firstAlignment.mate.strand}hasTag(t){return this.firstAlignment.hasTag(t)||this.secondAlignment&&this.secondAlignment.hasTag(t)}}class Kc{constructor(){this.alignments=[],this.score=void 0}findAlignment(t){const e=(t,e)=>e>=t.start&&e=r.start&&t0?c-=t:0===c&&(c=1)}return c}(r,n,t);case"STRAND":return r.strand?1:-1;case"START":return r.start;case"TAG":return r.tags()[i];case"READ_NAME":return r.readName;case"INSERT_SIZE":return-Math.abs(r.fragmentLength);case"GAP_SIZE":return-r.gapSizeAt(t);case"MATE_CHR":return r.mate;case"MQ":return void 0===r.mq?Number.MAX_VALUE:-r.mq;case"ALIGNED_READ_LENGTH":return-r.lengthOnRef;default:return Number.MAX_VALUE}}}function Jc(t){return t.isPaired()&&t.mate&&t.isMateMapped()&&t.chr===t.mate.chr&&(t.isFirstOfPair()||t.isSecondOfPair())&&!(t.isSecondary()||t.isSupplementary())}function tu(t){const e=[];for(let i of t)for(let t of i.alignments)t instanceof Xc?(t.firstAlignment&&e.push(t.firstAlignment),t.secondAlignment&&e.push(t.secondAlignment)):e.push(t);return e}function eu(t,e,i,n){if(t){if(0===t.length)return[];{t.sort((function(t,e){return n?t.scStart-e.scStart:t.start-e.start}));const e=[];let i,r=0,s=0;const o=new Set,a=()=>{i=new Kc,e.push(i),r=0,s=0,o.clear()};for(a();t.length>0;)if(s>=0&&s(n?t.scStart:t.start)>r),s)}else t=t.filter((t=>!o.has(t))),a();return e}}}function iu(t,e,i){let n=i-1,r=t.length;for(;1+n>1);e(t[i])?r=i:n=i}return r}class nu{constructor(t,e,i,{samplingWindowSize:n,samplingDepth:r,pairsSupported:s,alleleFreqThreshold:o}){this.chr=t,this.start=Math.floor(e),this.end=Math.ceil(i),this.length=i-e,this.alleleFreqThreshold=void 0===o?.2:o,this.coverageMap=new su(t,e,i,this.alleleFreqThreshold),this.alignments=[],this.downsampledIntervals=[],this.samplingWindowSize=void 0===n?100:n,this.samplingDepth=void 0===r?1e3:r,this.pairsSupported=void 0===s||s,this.paired=!1,this.pairsCache={},this.downsampledReads=new Set,this.currentBucket=new ru(this.start,this.start+this.samplingWindowSize,this),this.filter=function(t){return t.isMapped()&&!t.isFailsVendorQualityCheck()}}push(t){!1!==this.filter(t)&&(this.coverageMap.incCounts(t),this.pairsSupported&&this.downsampledReads.has(t.readName)||(t.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new ru(t.start,t.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(t)))}forEach(t){this.alignments.forEach(t)}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.alignments.sort((function(t,e){return t.start-e.start})),this.pairsCache=void 0,this.downsampledReads=void 0}contains(t,e,i){return this.chr===t&&this.start<=e&&this.end>=i}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new au(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount)),this.paired=this.paired||this.currentBucket.paired}setViewAsPairs(t){let e;e=t?function(t){const e={},i=[];for(let n of t)for(let t of n.alignments)if(Jc(t)){let n=e[t.readName];n?(n.setSecondAlignment(t),e[t.readName]=void 0):(n=new Xc(t),e[t.readName]=n,i.push(n))}else i.push(t);return i}(this.packedAlignmentRows):tu(this.packedAlignmentRows),this.packedAlignmentRows=eu(e,this.start,this.end)}setShowSoftClips(t){const e=this.allAlignments();this.packedAlignmentRows=eu(e,this.start,this.end,t)}repack(t,e){const i=this.allAlignments();this.packedAlignmentRows=eu(i,this.start,this.end,e)}allAlignments(){const t=[];for(let e of this.packedAlignmentRows)for(let i of e.alignments)t.push(i);return t}getMax(t,e){return this.coverageMap.getMax(t,e)}sortRows(t){const e=[],i=[];for(let n of this.packedAlignmentRows)void 0!==n.findAlignment(t.position)?e.push(n):i.push(n);e.sort(((e,i)=>{const n=t.direction,r=e.getSortValue(t,this),s=i.getSortValue(t,this);if(void 0===s&&void 0!==s)return 1;if(void 0!==r&&void 0===s)return-1;const o=r>s?1:re)break;const s=this.coverage[r];n>=t&&s&&(i=Math.max(i,s.total))}return i}incCounts(t){var e=this;if(void 0===t.blocks?i(t):t.blocks.forEach((function(t){i(t)})),t.gaps)for(let i of t.gaps)if("D"===i.type){const t=i.start-e.bpStart;for(let n=t;n=e}}class au{constructor(t,e,i){this.start=t,this.end=e,this.counts=i}popupData(t){return[{name:"start",value:this.start+1},{name:"end",value:this.end},{name:"# downsampled:",value:this.counts}]}}class lu{constructor(t){const e=t.split(",");this.chr=e[0],this.start=parseInt(e[1]),this.strand=e[2].charAt(0),this.mapQ=parseInt(e[4]),this.numMismatches=parseInt(e[5]),this.lenOnRef=Cu.computeLengthOnReference(e[3])}printString(){return this.chr+":"+$i(this.start)+"-"+$i(this.start+this.lenOnRef)+" ("+this.strand+") = "+$i(this.lenOnRef)+"bp @MAPQ: "+this.mapQ+" NM: "+this.numMismatches}}function hu(t){return t.split(";").filter((t=>t.length>0)).map((t=>new lu(t)))}const cu={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class uu{constructor(){this.hidden=!1}isMapped(){return 0==(4&this.flags)}isPaired(){return 0!=(1&this.flags)}isProperPair(){return 0!=(2&this.flags)}isFirstOfPair(){return 0!=(64&this.flags)}isSecondOfPair(){return 0!=(128&this.flags)}isSecondary(){return 0!=(256&this.flags)}isSupplementary(){return 0!=(2048&this.flags)}isFailsVendorQualityCheck(){return 0!=(512&this.flags)}isDuplicate(){return 0!=(1024&this.flags)}isMateMapped(){return 0==(8&this.flags)}isNegativeStrand(){return 0!=(16&this.flags)}isMateNegativeStrand(){return 0!=(32&this.flags)}hasTag(t){return(this.tagDict||fu(this.tagBA)).hasOwnProperty(t)}tags(){return this.tagDict||(this.tagBA?(this.tagDict=fu(this.tagBA),this.tagBA=void 0):this.tagDict={}),this.tagDict}containsLocation(t,e){const i=e?this.scStart:this.start,n=e?this.scLengthOnRef:this.lengthOnRef;return t>=i&&t<=i+n}popupData(t){const e=[];if(t=Math.floor(t),this.insertions){const n=this.seq;for(let r of this.insertions){var i=r.start;if(t===i||t===i-1)return e.push({name:"Insertion",value:n.substr(r.seqOffset,r.len)}),e.push({name:"Location",value:i}),e}}e.push({name:"Read Name",value:this.readName}),e.push("
"),e.push({name:"Alignment Start",value:$i(1+this.start),borderTop:!0}),e.push({name:"Read Strand",value:!0===this.strand?"(+)":"(-)",borderTop:!0});let n=this.cigar;if(n&&n.length>50){const t=25;n=`${n.substring(0,t-2)} ... ${n.substring(n.length-t+2)}`}e.push({name:"Cigar",value:n}),e.push({name:"Mapping Quality",value:this.mq}),e.push({name:"Secondary",value:o(this.isSecondary())}),e.push({name:"Supplementary",value:o(this.isSupplementary())}),e.push({name:"Duplicate",value:o(this.isDuplicate())}),e.push({name:"Failed QC",value:o(this.isFailsVendorQualityCheck())}),this.isPaired()&&(e.push("
"),e.push({name:"First in Pair",value:!this.isSecondOfPair(),borderTop:!0}),e.push({name:"Mate is Mapped",value:o(this.isMateMapped())}),this.pairOrientation&&e.push({name:"Pair Orientation",value:this.pairOrientation}),this.isMateMapped()&&(e.push({name:"Mate Chromosome",value:this.mate.chr}),e.push({name:"Mate Start",value:this.mate.position+1}),e.push({name:"Mate Strand",value:!0===this.mate.strand?"(+)":"(-)"}),e.push({name:"Insert Size",value:this.fragmentLength})));const r=this.tags();if(r.hasOwnProperty("SA")){e.push("
"),e.push({name:"Supplementary Alignments",value:""});const t=hu(r.SA);if(t){e.push("
    ");for(let i of t)e.push(`
  • ${i.printString()}
  • `);e.push("
")}}const s=new Set(["SA","MD"]);e.push("
");for(let t in r)s.has(t)||e.push({name:t,value:r[t]});return e.push({name:"Hidden Tags",value:"SA, MD"}),e.push("
"),e.push({name:"Genomic Location: ",value:$i(1+t)}),e.push({name:"Read Base:",value:this.readBaseAt(t)}),e.push({name:"Base Quality:",value:this.readBaseQualityAt(t)}),e;function o(t){return t?"Yes":"No"}}readBaseAt(t){const e=du(this.blocks,t);if(e){if("*"===this.seq)return"*";{const i=e.seqIndexAt(t);return this.seq[i]}}}readBaseQualityAt(t){const e=du(this.blocks,t);if(e){if("*"===this.qual)return 30;{const i=e.seqIndexAt(t);return i>=0&&this.qual&&i=e.start&&t=n.start&&e>1)+n;a+4=e)return!1;if("B"!==String.fromCharCode(t[a+2])||"I"!==String.fromCharCode(t[a+3]))return!1;var h=Tu(t,a+4),c=a+8;if(c+4*h>e)return!1;var u="",d=0;s.length=0,a=c;for(var f=0;f>4,m=xu[15&p];"M"!==m&&"EQ"!==m&&"X"!==m&&"D"!==m&&"N"!==m&&"="!==m||(d+=g),u=u+g+m,s.push({len:g,ltr:m})}return r.cigar=u,r.lengthOnRef=d,!0},decodeBamRecords:function(t,e,i,n,r,s,o,a){for(;et.length)return;if(p<0){e=d;continue}if(void 0!==r&&(p>r||g>o))return!0;if(void 0!==r&&p>8,y=255&m,v=Tu(t,e+16),w=(4294901760&v)>>16,_=65535&v,x=Tu(t,e+20),k=Tu(t,e+24),S=Tu(t,e+28),C=Tu(t,e+32);let A=[];for(let i=0;i>4,c=xu[15&l];"M"!==c&&"EQ"!==c&&"X"!==c&&"D"!==c&&"N"!==c&&"="!==c||(T+=h),I=I+h+c,E+=4,R={len:h,ltr:c},M.push(R)}if(f.chr=n[p],f.start=g,f.flags=w,f.strand=!(16&w),f.readName=A,f.cigar=I,f.lengthOnRef=T,f.fragmentLength=C,f.mq=b,Cu.bam_tag2cigar(t,d,E,x,f,M),f.end=f.start+f.lengthOnRef,f.end>1;for(let e=0;e>4]),L.push(_u[15&u])}L=L.slice(0,x).join(""),E+=B;const N=[];for(let e=0;e=0&&(f.mate={chr:n[k],position:S,strand:!(32&w)}),f.seq=L,f.qual=N,f.tagBA=new Uint8Array(t.buffer.slice(E,d)),this.setPairOrientation(f),(void 0===a||a.pass(f))&&(Au(f,M),i.push(f)),e=d}},decodeSamRecords:function(t,e,i,n,r,s){var o,a,l,h,c,u,d,f,p,g;for(h=(o=qi(t)).length,a=0;ar)break;if(f=0,(g=Iu(p.cigar)).forEach((function(t){var e=t.len,i=t.ltr;"M"!==i&&"EQ"!==i&&"X"!==i&&"D"!==i&&"N"!==i&&"="!==i||(f+=e)})),p.lengthOnRef=f,!(p.start+fSu&&(console.log("Warning: attempt to set sampling depth > maximum value of "+Su),t.samplingDepth=Su),e.viewAsPairs?t.pairsSupported=!0:t.pairsSupported=void 0===e.pairsSupported||e.pairsSupported},setPairOrientation:function(t){if(t.isMapped()&&t.mate&&t.isMateMapped()&&t.mate.chr===t.chr){var e=t.strand?"F":"R",i=t.mate,n=i.strand?"F":"R",r=" ",s=" ";t.isFirstOfPair()?(r="1",s="2"):t.isSecondOfPair()&&(r="2",s="1");var o=[],a=t.fragmentLength,l=t.end-t.start;0===a&&(a=(t.start0?(o[0]=e,o[1]=r,o[2]=n,o[3]=s):(o[2]=e,o[3]=r,o[0]=n,o[1]=s),t.pairOrientation=o.join("")}},computeLengthOnReference:function(t){let e=0,i="";for(let n=0;n47&&r<58)i+=t.charAt(n);else{switch(r){case 78:case 68:case 77:case 61:case 88:e+=parseInt(i.toString())}i=""}}return e}};function Au(t,e){const i=[];let n,r,s=0,o=t.start;t.scStart=t.start,t.scLengthOnRef=t.lengthOnRef;for(let a of e){let e;switch(a.ltr){case"H":case"P":break;case"S":e=o,t.scLengthOnRef+=a.len,0===i.length&&(t.scStart-=a.len,e-=a.len),i.push(new vu({start:e,seqOffset:s,len:a.len,type:"S"})),s+=a.len;break;case"N":case"D":void 0===r&&(r=[]),r.push({start:o,len:a.len,type:a.ltr}),o+=a.len;break;case"I":void 0===n&&(n=[]),n.push(new vu({start:o,len:a.len,seqOffset:s,type:"I"})),s+=a.len;break;case"M":case"EQ":case"=":case"X":i.push(new vu({start:o,seqOffset:s,len:a.len,type:"M"})),s+=a.len,o+=a.len;break;default:console.log("Error processing cigar element: "+a.len+a.ltr)}}t.blocks=i,t.insertions=n,t.gaps=r}function Tu(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function Iu(t){var e,i,n,r,s,o,a,l,h;for(e=[],i=[],s=null,r=t.length,n=0;n=48&&h<=57?i.push(o):(a=o,l=Number.parseInt(i.join("")),i=[],null!==s&&s.ltr===a?s.len+=l:(s={len:l,ltr:a},e.push(s)));return e}function Eu(t){var e={};return t.forEach((function(t){var i=t.split(":");e[i[0]]=i[2]})),e}class Mu{constructor(t,e){this.config=t,this.genome=e,this.bamPath=t.url,this.isDataUri=fa(t.url),Cu.setReaderDefaults(this,t)}async readAlignments(t,e,i){if(this.alignmentCache){const n=this.header,r=n.chrAliasTable.hasOwnProperty(t)?n.chrAliasTable[t]:t,s=this.alignmentCache.queryFeatures(r,e,i),o=new nu(t,e,i,this.config);for(let t of s)o.push(t);return o.finish(),o}if(this.isDataUri){const n=uo(function(t){const e=t.split(","),i=e[0].split(":")[1];let n=e[1];n=i.indexOf("base64")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s{var t={368:function(t,e,i){var n=this&&this.__awaiter||function(t,e,i,n){return new(i||(i=Promise))((function(r,s){function o(t){try{l(n.next(t))}catch(t){s(t)}}function a(t){try{l(n.throw(t))}catch(t){s(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof i?e:new i((function(t){t(e)}))).then(o,a)}l((n=n.apply(t,e||[])).next())}))},r=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const s=r(i(4105)),o=r(i(1269)),a=i(597),l=i(3427),h=i(8577);function c(t,e){if(e.some((t=>void 0===t)))throw new h.CramMalformedError("invalid .crai index file");const[i,n,r,s,o,a]=e;t[i]||(t[i]=[]),t[i].push({start:n,span:r,containerStart:s,sliceStart:o,sliceBytes:a})}e.default=class{constructor(t){this.filehandle=(0,l.open)(t.url,t.path,t.filehandle),this._parseCache=new s.default({cache:new o.default({maxSize:1}),fill:(t,e)=>this.parseIndex()})}parseIndex(){const t={};return this.filehandle.readFile().then((t=>31===t[0]&&139===t[1]?(0,a.unzip)(t):t)).then((e=>{if(e.length>4&&21578050===e.readUInt32LE(0))throw new h.CramMalformedError("invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support");let i=[],n="";for(let r=0;r=48&&s<=57||!n&&45===s)n+=String.fromCharCode(s);else if(9===s)i.push(Number.parseInt(n,10)),n="";else if(10===s)i.push(Number.parseInt(n,10)),n="",c(t,i),i=[];else if(13!==s&&32!==s)throw new h.CramMalformedError("invalid .crai index file")}return n&&i.push(Number.parseInt(n,10)),6===i.length&&c(t,i),Object.entries(t).forEach((([e,i])=>{t[e]=i.sort(((t,e)=>t.start-e.start||t.span-e.span))})),t}))}getIndex(t={}){return this._parseCache.get("index",null,t.signal)}hasDataForReferenceSequence(t){return n(this,void 0,void 0,(function*(){return!!(yield this.getIndex())[t]}))}getEntriesForRange(t,e,i){return n(this,void 0,void 0,(function*(){const n=(yield this.getIndex())[t];if(!n)return[];const r=t=>{const n=t.start,r=t.start+t.span;return n>i?-1:r<=e?1:0},s=[];for(let t=0;t{Object.defineProperty(e,"__esModule",{value:!0}),e.default=class{constructor(t,e){this.parameters=t,this.dataType=e}}},4863:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=i(8577),s=n(i(1050)),o=i(1074);class a extends s.default{constructor(t,e){if(super(t,e),"int"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`)}decode(t,e,i,n){return(0,o.getBits)(e.content,n.coreBlock,this.parameters.length)-this.parameters.offset}}e.default=a},1738:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=i(9488),s=n(i(1050));class o extends s.default{constructor(t,e,i){if(super(t,e),this.instantiateCodec=i,"byteArray"!==e)throw new TypeError(`byteArrayLength does not support data type ${e}`)}decode(t,e,i,n){const r=this._getLengthCodec().decode(t,e,i,n),s=this._getDataCodec(),o=new Uint8Array(r);for(let a=0;a(0,r.tinyMemoize)(o,t)))},1405:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=i(8577),s=n(i(1050)),o=i(1074);class a extends s.default{constructor(t,e){if(super(t,e),"byteArray"!==e)throw new TypeError(`byteArrayStop codec does not support data type ${e}`)}decode(t,e,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}`);const a=n.externalBlocks.getCursor(s);return this._decodeByteArray(o,a)}_decodeByteArray(t,e){const i=t.content,{stopByte:n}=this.parameters,r=e.bytePosition;let s=e.bytePosition;for(;i[s]!==n&&s=t.content.length)throw new a.CramBufferOverrunError("attempted to read beyond end of block. this file seems truncated.");return t.content[e.bytePosition++]}}e.default=l},4229:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=i(8577),s=n(i(1050)),o=i(1074);class a extends s.default{constructor(t,e){if(super(t,e),"int"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`)}decode(t,e,i,n){let r=1;for(;0===(0,o.getBits)(e.content,n.coreBlock,1);)r+=1;return((0,o.getBits)(e.content,n.coreBlock,r-1)|1<{Object.defineProperty(e,"__esModule",{value:!0}),e.getBits=e.CramBufferOverrunError=void 0;class i extends Error{}e.CramBufferOverrunError=i,e.getBits=function(t,e,n){let r=0;if(e.bytePosition+(7-e.bitPosition+n)/8>t.length)throw new i("read error during decoding. the file seems to be truncated.");for(let i=n;i;i--)r<<=1,r|=t[e.bytePosition]>>e.bitPosition&1,e.bitPosition-=1,e.bitPosition<0&&(e.bytePosition+=1),e.bitPosition&=7;return r}},2082:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=i(8577),s=n(i(1050)),o=i(1074);class a extends s.default{constructor(t,e){if(super(t,e),this.codes={},this.codeBook={},this.sortedByValue=[],this.sortedCodes=[],this.sortedValuesByBitCode=[],this.sortedBitCodes=[],this.sortedBitLengthsByBitCode=[],this.bitCodeToValue=[],!["byte","int"].includes(this.dataType))throw new TypeError(`${this.dataType} decoding not yet implemented by HUFFMAN_INT codec`);this.buildCodeBook(),this.buildCodes(),this.buildCaches(),0===this.sortedCodes[0].bitLength&&(this._decode=this._decodeZeroLengthCode)}buildCodeBook(){let t=new Array(this.parameters.numCodes);for(let e=0;et.bitLength-e.bitLength||t.symbol-e.symbol)),this.codeBook={},t.forEach((t=>{this.codeBook[t.bitLength]||(this.codeBook[t.bitLength]=[]),this.codeBook[t.bitLength].push(t.symbol)}))}buildCodes(){this.codes={};let t=0,e=-1;Object.entries(this.codeBook).forEach((([i,n])=>{const s=parseInt(i,10);n.forEach((i=>{const n={bitLength:s,value:i,bitCode:0};e+=1;const o=s-t;if(e<<=o,n.bitCode=e,t+=o,function(t){let e=t-(t>>1)&1431655765;return e=(858993459&e)+(e>>2&858993459),16843009*(e+(e>>4)&252645135)>>24}(e)>s)throw new r.CramMalformedError("Symbol out of range");this.codes[i]=n}))}))}buildCaches(){this.sortedCodes=Object.values(this.codes).sort(((t,e)=>t.bitLength-e.bitLength||t.bitCode-e.bitCode)),this.sortedByValue=Object.values(this.codes).sort(((t,e)=>t.value-e.value)),this.sortedValuesByBitCode=this.sortedCodes.map((t=>t.value)),this.sortedBitCodes=this.sortedCodes.map((t=>t.bitCode)),this.sortedBitLengthsByBitCode=this.sortedCodes.map((t=>t.bitLength));const t=Math.max(...this.sortedBitCodes);this.bitCodeToValue=new Array(t+1).fill(-1);for(let t=0;t-1&&this.sortedBitLengthsByBitCode[i]===e)return this.sortedValuesByBitCode[i];for(let i=t;this.sortedCodes[i+1].bitLength===e&&i{Object.defineProperty(e,"__esModule",{value:!0}),e.default={CRAM_FLAG_PRESERVE_QUAL_SCORES:1,CRAM_FLAG_DETACHED:2,CRAM_FLAG_MATE_DOWNSTREAM:4,CRAM_FLAG_NO_SEQ:8,CRAM_FLAG_MASK:15,CRAM_M_REVERSE:1,CRAM_M_UNMAP:2,BAM_FPAIRED:1,BAM_FPROPER_PAIR:2,BAM_FUNMAP:4,BAM_FMUNMAP:8,BAM_FREVERSE:16,BAM_FMREVERSE:32,BAM_FREAD1:64,BAM_FREAD2:128,BAM_FSECONDARY:256,BAM_FQCFAIL:512,BAM_FDUP:1024,BAM_FSUPPLEMENTARY:2048,BAM_CMATCH:0,BAM_CINS:1,BAM_CDEL:2,BAM_CREF_SKIP:3,BAM_CSOFT_CLIP:4,BAM_CHARD_CLIP:5,BAM_CPAD:6,BAM_CEQUAL:7,BAM_CDIFF:8,BAM_CBACK:9,BAM_CIGAR_STR:"MIDNSHP:XB",BAM_CIGAR_SHIFT:4,BAM_CIGAR_MASK:15,BAM_CIGAR_TYPE:246183}},8543:(t,e,i)=>{Object.defineProperty(e,"__esModule",{value:!0});const n=i(8772),r=i(8577),s={BF:"int",CF:"int",RI:"int",RL:"int",AP:"int",RG:"int",MF:"int",NS:"int",NP:"int",TS:"int",NF:"int",TC:"byte",TN:"int",FN:"int",FC:"byte",FP:"int",BS:"byte",IN:"byteArray",SC:"byteArray",DL:"int",BA:"byte",BB:"byteArray",RS:"int",PD:"int",HC:"int",MQ:"int",RN:"byteArray",QS:"byte",QQ:"byteArray",TL:"int"};e.default=class{constructor(t){this.dataSeriesCodecCache={},this.tagCodecCache={},this.tagEncoding={},this.readNamesIncluded=t.preservation.RN,this.APdelta=t.preservation.AP,this.referenceRequired=!!t.preservation.RR,this.tagIdsDictionary=t.preservation.TD,this.substitutionMatrix=function(t){const e=new Array(5);for(let t=0;t<5;t+=1)e[t]=new Array(4);return e[0][t[0]>>6&3]="C",e[0][t[0]>>4&3]="G",e[0][t[0]>>2&3]="T",e[0][t[0]>>0&3]="N",e[1][t[1]>>6&3]="A",e[1][t[1]>>4&3]="G",e[1][t[1]>>2&3]="T",e[1][t[1]>>0&3]="N",e[2][t[2]>>6&3]="A",e[2][t[2]>>4&3]="C",e[2][t[2]>>2&3]="T",e[2][t[2]>>0&3]="N",e[3][t[3]>>6&3]="A",e[3][t[3]>>4&3]="C",e[3][t[3]>>2&3]="G",e[3][t[3]>>0&3]="N",e[4][t[4]>>6&3]="A",e[4][t[4]>>4&3]="C",e[4][t[4]>>2&3]="G",e[4][t[4]>>0&3]="T",e}(t.preservation.SM),this.dataSeriesEncoding=t.dataSeriesEncoding,this.tagEncoding=t.tagEncoding,this.preservation=t.preservation,this._size=t._size,this._endPosition=t._endPosition}getCodecForTag(t){if(!this.tagCodecCache[t]){const e=this.tagEncoding[t];e&&(this.tagCodecCache[t]=(0,n.instantiateCodec)(e,"byteArray"))}return this.tagCodecCache[t]}getTagNames(t){return this.tagIdsDictionary[t]}getCodecForDataSeries(t){let e=this.dataSeriesCodecCache[t];if(void 0===e){const i=this.dataSeriesEncoding[t];if(i){const o=s[t];if(!o)throw new r.CramMalformedError(`data series name ${t} not defined in 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t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const s=i(597),o=r(i(2779)),a=r(i(1269)),l=i(8577),h=r(i(9675)),c=i(6141),u=r(i(3498)),d=r(i(6284)),f=i(3427),p=i(9488),g=i(7578);class m{constructor(t){var e;if(this.file=(0,f.open)(t.url,t.path,t.filehandle),this.validateChecksums=!0,this.fetchReferenceSequenceCallback=t.seqFetch,this.options={checkSequenceMD5:t.checkSequenceMD5,cacheSize:null!==(e=t.cacheSize)&&void 0!==e?e:2e4},this.featureCache=new a.default({maxSize:this.options.cacheSize}),function(){const t=new Uint32Array([287454020]),e=new Uint8Array(t.buffer);return 68===e[0]?0:17===e[0]?1:2}()>0)throw new Error("Detected big-endian machine, may be unable to run")}read(t,e,i,n){return this.file.read(t,e,i,n)}stat(){return this.file.stat()}getDefinition(){return n(this,void 0,void 0,(function*(){const t=Buffer.allocUnsafe(c.cramFileDefinition.maxLength);yield this.file.read(t,0,c.cramFileDefinition.maxLength,0);const e=c.cramFileDefinition.parser.parse(t).result;if(2!==e.majorVersion&&3!==e.majorVersion)throw new l.CramUnimplementedError(`CRAM version ${e.majorVersion} not supported`);return e}))}getSamHeader(){return n(this,void 0,void 0,(function*(){const t=yield this.getContainerById(0);if(!t)throw new l.CramMalformedError("file contains no containers");const e=yield t.getFirstBlock();if(void 0===e)return(0,g.parseHeaderText)("");const i=e.content,n=i.readInt32LE(0),r=i.toString("utf8",4,4+n);return this.header=r,(0,g.parseHeaderText)(r)}))}getHeaderText(){return n(this,void 0,void 0,(function*(){return yield this.getSamHeader(),this.header}))}getSectionParsers(){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition();return(0,c.getSectionParsers)(t)}))}getContainerById(t){return n(this,void 0,void 0,(function*(){const e=yield this.getSectionParsers();let i=e.cramFileDefinition.maxLength;const{size:n}=yield this.file.stat(),{cramContainerHeader1:r}=e;let s;for(let e=0;e<=t;e+=1){if(i+r.maxLength+8>=n)return;s=this.getContainerAtPosition(i);const o=yield s.getHeader();if(!o)throw new l.CramMalformedError(`container ${t} not found in file`);if(0===e){i=o._endPosition;for(let t=0;t=n)return;const r=Buffer.allocUnsafe(i.maxLength);return yield this.file.read(r,0,i.maxLength,t),(0,p.parseItem)(r,i.parser,0,t)}))}_parseSection(t,e,i=t.maxLength,r){return n(this,void 0,void 0,(function*(){let n;if(r)n=r;else{const{size:t}=yield this.file.stat();if(e+i>=t)return;n=Buffer.allocUnsafe(i),yield this.file.read(n,0,i,e)}const s=(0,p.parseItem)(n,t.parser,0,e);if(s._size!==i)throw new l.CramMalformedError(`section read error: requested size ${i} does not equal parsed size ${s._size}`);return s}))}_uncompress(t,e,i){if("gzip"===t)(0,s.unzip)(e).copy(i);else if("bzip2"===t){const t=bzip2.array(e);let n,r=bzip2.header(t),s=0;do{n=bzip2.decompress(t,r),-1!=n&&(Buffer.from(n).copy(i,s),s+=n.length,r-=n.length)}while(-1!=n)}else if("rans"===t)(0,h.default)(e,i);else if("rans4x16"===t)u.default.r4x16_uncompress(e,i);else if("arith"===t)u.default.arith_uncompress(e,i);else if("fqzcomp"===t)u.default.fqzcomp_uncompress(e,i);else{if("tok3"!==t)throw new l.CramUnimplementedError(`${t} decompression not yet implemented`);u.default.tok3_uncompress(e,i)}}readBlock(t){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.getDefinition(),i=yield this.getSectionParsers(),n=yield this.readBlockHeader(t);if(void 0===n)return;const r=n._endPosition,s=Buffer.allocUnsafe(n.uncompressedSize),o=Object.assign(Object.assign({},n),{_endPosition:r,contentPosition:r,content:s});if("raw"!==n.compressionMethod){const t=Buffer.allocUnsafe(n.compressedSize);yield this.read(t,0,n.compressedSize,r),this._uncompress(n.compressionMethod,t,s)}else yield this.read(s,0,n.uncompressedSize,r);if(e>=3){const e=yield this._parseSection(i.cramBlockCrc32,r+n.compressedSize);if(void 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r=n(i(2615)),s={a:0,A:0,c:1,C:1,g:2,G:2,t:3,T:3,n:4,N:4};function o(t){const e={};for(const[i,n]of t)e["is"+n]=t=>!!(t&i),e["set"+n]=t=>t|i;return e}e.BamFlags=[[1,"Paired"],[2,"ProperlyPaired"],[4,"SegmentUnmapped"],[8,"MateUnmapped"],[16,"ReverseComplemented"],[32,"MateReverseComplemented"],[64,"Read1"],[128,"Read2"],[256,"Secondary"],[512,"FailedQc"],[1024,"Duplicate"],[2048,"Supplementary"]],e.CramFlags=[[1,"PreservingQualityScores"],[2,"Detached"],[4,"WithMateDownstream"],[8,"DecodeSequenceAsStar"]],e.MateFlags=[[1,"OnNegativeStrand"],[2,"Unmapped"]],e.BamFlagsDecoder=o(e.BamFlags),e.CramFlagsDecoder=o(e.CramFlags),e.MateFlagsDecoder=o(e.MateFlags),e.default=class{constructor({flags:t,cramFlags:e,readLength:i,mappingQuality:n,lengthOnRef:r,qualityScores:s,mateRecordNumber:o,readBases:a,readFeatures:l,mateToUse:h,readGroupId:c,readName:u,sequenceId:d,uniqueId:f,templateSize:p,alignmentStart:g,tags:m}){this.flags=t,this.cramFlags=e,this.readLength=i,this.mappingQuality=n,this.lengthOnRef=r,this.qualityScores=s,a&&(this.readBases=a),this.readGroupId=c,this.readName=u,this.sequenceId=d,this.uniqueId=f,this.templateSize=p,this.alignmentStart=g,this.tags=m,l&&(this.readFeatures=l),h&&(this.mate={flags:h.mateFlags,readName:h.mateReadName,sequenceId:h.mateSequenceId,alignmentStart:h.mateAlignmentStart}),o&&(this.mateRecordNumber=o)}isPaired(){return!!(this.flags&r.default.BAM_FPAIRED)}isProperlyPaired(){return!!(this.flags&r.default.BAM_FPROPER_PAIR)}isSegmentUnmapped(){return!!(this.flags&r.default.BAM_FUNMAP)}isMateUnmapped(){return!!(this.flags&r.default.BAM_FMUNMAP)}isReverseComplemented(){return!!(this.flags&r.default.BAM_FREVERSE)}isMateReverseComplemented(){return!!(this.flags&r.default.BAM_FMREVERSE)}isRead1(){return!!(this.flags&r.default.BAM_FREAD1)}isRead2(){return!!(this.flags&r.default.BAM_FREAD2)}isSecondary(){return!!(this.flags&r.default.BAM_FSECONDARY)}isFailedQc(){return!!(this.flags&r.default.BAM_FQCFAIL)}isDuplicate(){return!!(this.flags&r.default.BAM_FDUP)}isSupplementary(){return!!(this.flags&r.default.BAM_FSUPPLEMENTARY)}isDetached(){return!!(this.cramFlags&r.default.CRAM_FLAG_DETACHED)}hasMateDownStream(){return!!(this.cramFlags&r.default.CRAM_FLAG_MATE_DOWNSTREAM)}isPreservingQualityScores(){return!!(this.cramFlags&r.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)}isUnknownBases(){return!!(this.cramFlags&r.default.CRAM_FLAG_NO_SEQ)}getReadBases(){if(!this.readBases&&this._refRegion){const t=function(t,e){if(!t.lengthOnRef&&!t.readLength)return null;if(t.isUnknownBases())return null;const i=t.alignmentStart-e.start;if(!t.readFeatures)return e.seq.substr(i,t.lengthOnRef).toUpperCase();let n="",r=i,s=0;for(;n.lengththis.mate.alignmentStart&&s>0&&(s=-s),s>0?(r[0]=t,r[1]=i,r[2]=e,r[3]=n):(r[2]=t,r[3]=i,r[0]=e,r[1]=n),r.join("")}return null}addReferenceSequence(t,e){this.readFeatures&&this.readFeatures.forEach((i=>{"X"===i.code&&function(t,e,i,n){if(!e)return;const r=n.refPos-e.start,o=e.seq.charAt(r);o&&(n.ref=o);let a=s[o];void 0===a&&(a=4);const l=i.substitutionMatrix[a][n.data];l&&(n.sub=l)}(0,t,e,i)})),!this.readBases&&t.start<=this.alignmentStart&&t.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=t)}toJSON(){const t={};return Object.keys(this).forEach((e=>{"_"!==e.charAt(0)&&(t[e]=this[e])})),t.readBases=this.getReadBases(),t}}},6141:(t,e,i)=>{Object.defineProperty(e,"__esModule",{value:!0}),e.getSectionParsers=e.cramFileDefinition=e.isMappedSliceHeader=void 0;const n=i(9996),r=(new n.Parser).itf8(),s={parser:(new n.Parser).string("magic",{length:4}).uint8("majorVersion").uint8("minorVersion").string("fileId",{length:20,stripNull:!0}),maxLength:26};e.cramFileDefinition=s;const o={parser:(new n.Parser).uint8("compressionMethod",{formatter:t=>{const e=["raw","gzip","bzip2","lzma","rans","rans4x16","arith","fqzcomp","tok3"][t];if(!e)throw new Error(`compression method number ${t} not implemented`);return e}}).uint8("contentType",{formatter:t=>{const e=["FILE_HEADER","COMPRESSION_HEADER","MAPPED_SLICE_HEADER","UNMAPPED_SLICE_HEADER","EXTERNAL_DATA","CORE_DATA"][t];if(!e)throw new Error(`invalid block content type id ${t}`);return e}}).itf8("contentId").itf8("compressedSize").itf8("uncompressedSize"),maxLength:17},a={parser:(new n.Parser).uint32("crc32"),maxLength:4},l=(new n.Parser).itf8("size").buffer("ents",{length:"size",formatter:t=>{function e(e,i){const n=t.toString("utf8",e,i),r=[];for(let t=0;tr&&n.push(e(r,i)),n}}),h=(new n.Parser).uint8(null,{formatter:t=>!!t}),c=(new n.Parser).itf8("mapSize").itf8("mapCount").array("ents",{length:"mapCount",type:(new n.Parser).string("key",{length:2,stripNull:!1}).choice("value",{tag:"key",choices:{MI:h,UI:h,PI:h,RN:h,AP:h,RR:h,SM:(new n.Parser).array(null,{type:"uint8",length:5}),TD:(new n.Parser).nest(null,{type:l,formatter:t=>t.ents})}})});function u(t){const e={};for(let i=0;i=3?(i=i.ltf8("recordCounter"),e+=9):2===t&&(i=i.itf8("recordCounter"),e+=5),i=i.itf8("numBlocks").itf8("numContentIds").array("contentIds",{type:r,length:"numContentIds"}),e+=10,t>=2&&(i=i.array("md5",{type:"uint8",length:16}),e+=16),{parser:i,maxLength:t=>e+5*t}},cramMappedSliceHeader(t){let e=(new n.Parser).itf8("refSeqId").itf8("refSeqStart").itf8("refSeqSpan").itf8("numRecords"),i=20;return t>=3?(e=e.ltf8("recordCounter"),i+=9):2===t&&(e=e.itf8("recordCounter"),i+=5),e=e.itf8("numBlocks").itf8("numContentIds").array("contentIds",{type:r,length:"numContentIds"}).itf8("refBaseBlockId"),i+=15,t>=2&&(e=e.array("md5",{type:"uint8",length:16}),i+=16),{parser:e,maxLength:t=>i+5*t}},cramEncoding:t=>({parser:(new n.Parser).namely("cramEncoding").itf8("codecId").itf8("parametersBytes").choice("parameters",{tag:"codecId",choices:{0:new n.Parser,1:(new n.Parser).itf8("blockContentId"),2:(new 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t>=3&&(e=e.uint32("crc32"),i=4),{parser:e,maxLength:t=>5+5*t+i}}};e.getSectionParsers=function(t){const e=Object.assign({},d);return Object.keys(f).forEach((i=>{e[i]=f[i](t)})),e}},3757:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=n(i(3720)),s=i(8577),o=i(8631),a=i(6141);function l(t){let e="";for(let i=0;i1&&-2===n.parsedContent.refSeqId?e("RI"):n.parsedContent.refSeqId;const b=e("RL");let y=e("AP");i.APdelta&&(y+=u.lastAlignmentStart),u.lastAlignmentStart=y;const v=e("RG");let w,_,x,k;if(i.readNamesIncluded&&(w=l(e("RN"))),o.CramFlagsDecoder.isDetached(g)){const t=e("MF");let n;i.readNamesIncluded||(n=l(e("RN")),w=n);const r=e("NS"),s=e("NP");(t||r>-1)&&(_={mateFlags:t,mateSequenceId:r,mateAlignmentStart:s,mateReadName:n}),x=e("TS"),o.MateFlagsDecoder.isUnmapped(t)&&(p=o.BamFlagsDecoder.setMateUnmapped(p)),o.MateFlagsDecoder.isOnNegativeStrand(t)&&(p=o.BamFlagsDecoder.setMateReverseComplemented(p))}else o.CramFlagsDecoder.isWithMateDownstream(g)&&(k=e("NF")+f+1);const S=e("TL");if(S<0)throw new s.CramMalformedError("invalid TL index");const C={},A=i.getTagNames(S),T=A.length;for(let e=0;e1?"SC":"IN"],X:["number","BS"],D:["number","DL"],I:["string","IN"],i:["character","BA"],b:["string","BB"],q:["numArray","QQ"],Q:["number","QS"],H:["number","HC"],P:["number","PD"],N:["number","RS"]}[e];if(!c)throw new s.CramMalformedError(`invalid read feature code "${e}"`);let u=h(c);const d={B:["number","QS"]}[e];d&&(u=[u,h(d)]),o+=n;const f=o;a+=n;const p=a;"D"===e||"N"===e?a+=u:"I"===e||"S"===e?a-=u.length:"i"===e&&(a-=1),l[t]={code:e,pos:f,refPos:p,data:u}}return l}(y,t,e,0,d)),E=b,I)for(const{code:t,data:e}of I)"D"===t||"N"===t?E+=e:"I"===t||"S"===t?E-=e.length:"i"===t&&(E-=1);if(Number.isNaN(E)&&(console.warn(`${w||`${m}:${y}`} record has invalid read features`),E=b),M=e("MQ"),o.CramFlagsDecoder.isPreservingQualityScores(g)){R=new Array(b);for(let t=0;t=0){const r=t[i.mateRecordNumber];if(!r)throw new s.CramMalformedError("intra-slice mate record not found, this file seems malformed");n.push(...e(r))}return n}(i),r=n.map((t=>t.alignmentStart)),o=n.map((t=>t.alignmentStart+t.readLength-1)),a=Math.max(...o)-Math.min(...r)+1;a>=0&&n.forEach((t=>{if(void 0!==t.templateLength)throw new s.CramMalformedError("mate pair group has some members that have template lengths already, this file seems malformed");t.templateLength=a}))}(t,0,i):function(t,e){const i=Math.min(t.alignmentStart,e.alignmentStart),n=Math.max(t.alignmentStart+t.readLength-1,e.alignmentStart+e.readLength-1)-i+1;t.templateLength=n,e.templateLength=n}(i,n)),delete i.mateRecordNumber}class f{constructor(t,e,i){this.container=t,this.containerPosition=e,this.file=t.file}getHeader(){return n(this,void 0,void 0,(function*(){const t=yield this.file.getSectionParsers(),e=yield this.container.getHeader(),i=yield this.file.readBlock(e._endPosition+this.containerPosition);if(void 0===i)throw new Error;if("MAPPED_SLICE_HEADER"===i.contentType){const n=(0,o.parseItem)(i.content,t.cramMappedSliceHeader.parser,0,e._endPosition);return Object.assign(Object.assign({},i),{parsedContent:n})}if("UNMAPPED_SLICE_HEADER"===i.contentType){const n=(0,o.parseItem)(i.content,t.cramUnmappedSliceHeader.parser,0,e._endPosition);return Object.assign(Object.assign({},i),{parsedContent:n})}throw new s.CramMalformedError(`error reading slice header block, invalid content type ${i.contentType}`)}))}getBlocks(){return n(this,void 0,void 0,(function*(){const t=yield this.getHeader();let e=t._endPosition;const i=new Array(t.parsedContent.numBlocks);for(let t=0;t{"EXTERNAL_DATA"===t.contentType&&(e[t.contentId]=t)})),e}))}getBlockByContentId(t){return n(this,void 0,void 0,(function*(){return(yield this._getBlocksContentIdIndex())[t]}))}getReferenceRegion(){return n(this,void 0,void 0,(function*(){const t=(yield this.getHeader()).parsedContent;if(!(0,c.isMappedSliceHeader)(t))throw new Error;if(t.refSeqId<0)return;const e=yield this.container.getCompressionScheme();if(void 0===e)throw new Error;if(t.refBaseBlockId>=0){const e=yield this.getBlockByContentId(t.refBaseBlockId);if(!e)throw new s.CramMalformedError("embedded reference specified, but reference block does not exist");return{seq:e.data.toString("utf8"),start:t.refSeqStart,end:t.refSeqStart+t.refSeqSpan-1,span:t.refSeqSpan}}if(e.referenceRequired||this.file.fetchReferenceSequenceCallback){if(!this.file.fetchReferenceSequenceCallback)throw new Error("reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence");const e=yield this.file.fetchReferenceSequenceCallback(t.refSeqId,t.refSeqStart,t.refSeqStart+t.refSeqSpan-1);if(e.length!==t.refSeqSpan)throw new s.CramArgumentError("seqFetch callback returned a reference sequence of the wrong length");return{seq:e,start:t.refSeqStart,end:t.refSeqStart+t.refSeqSpan-1,span:t.refSeqSpan}}}))}getAllRecords(){return this.getRecords((()=>!0))}_fetchRecords(){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.file.getDefinition(),e=yield this.container.getCompressionScheme();if(void 0===e)throw new Error;const i=yield this.getHeader();if(void 0===i)throw new Error;const n=yield this._getBlocksContentIdIndex();if(t>1&&this.file.options.checkSequenceMD5&&(0,c.isMappedSliceHeader)(i.parsedContent)&&i.parsedContent.refSeqId>=0&&"0000000000000000"!==i.parsedContent.md5.join("")){const t=yield this.getReferenceRegion();if(t){const{seq:e,start:n,end:r}=t,a=(0,o.sequenceMD5)(e),l=i.parsedContent.md5.map((t=>(t<16?"0":"")+t.toString(16))).join("");if(a!==l)throw new s.CramMalformedError(`MD5 checksum reference mismatch for ref ${i.parsedContent.refSeqId} pos ${n}..${r}. recorded MD5: ${l}, calculated MD5: ${a}`)}}const r=yield this.getCoreDataBlock(),a={lastAlignmentStart:(0,c.isMappedSliceHeader)(i.parsedContent)?i.parsedContent.refSeqStart:0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{map:new Map,getCursor(t){let e=this.map.get(t);return void 0===e&&(e={bitPosition:7,bytePosition:0},this.map.set(t,e)),e}}},f=t=>{const i=e.getCodecForDataSeries(t);if(!i)throw new s.CramMalformedError(`no codec defined for ${t} data series`);return i.decode(this,r,n,a)};let p=new Array(i.parsedContent.numRecords);for(let s=0;s!!t));break}throw t}for(let t=0;t=0&&d(p,t,p[t],p[e])}return p}))}getRecords(t){return n(this,void 0,void 0,(function*(){const e=this.container.filePosition+this.containerPosition;let i=this.file.featureCache.get(e.toString());i||(i=this._fetchRecords(),this.file.featureCache.set(e.toString(),i));const r=(yield i).filter(t);if(r.length&&this.file.fetchReferenceSequenceCallback){const t=yield this.getHeader();if((0,c.isMappedSliceHeader)(t.parsedContent)&&(t.parsedContent.refSeqId>=0||-2===t.parsedContent.refSeqId)){const e=t.parsedContent.refSeqId>=0?t.parsedContent.refSeqId:void 0,i=yield this.container.getCompressionScheme();if(void 0===i)throw new Error;const s={};for(let t=0;tn.end&&(n.end=o),r[t].alignmentStartn(this,void 0,void 0,(function*(){-1!==t.id&&t.start<=t.end&&(t.seq=yield this.file.fetchReferenceSequenceCallback(t.id,t.start,t.end))})))));for(let t=0;t(0,o.tinyMemoize)(f,t)))},9488:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0}),e.sequenceMD5=e.tinyMemoize=e.parseItem=e.parseItf8=e.itf8Size=void 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supported");const n=t,o=yield this.index.getEntriesForRange(n,e,i),a=o.map((t=>t.sliceBytes)).reduce(((t,e)=>t+e),0);if(a>this.fetchSizeLimit)throw new s.CramSizeLimitError(`data size of ${a.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);const l=n=>n.sequenceId===t&&n.alignmentStart<=i&&void 0!==n.lengthOnRef&&n.alignmentStart+n.lengthOnRef-1>=e,h=yield Promise.all(o.map((t=>this.getRecordsInSlice(t,l))));let c=Array.prototype.concat(...h);if(r.viewAsPairs){const t={},e={};for(let i=0;i{1===e&&(i[t]=!0)}));const s=[];for(let t=0;tt.toString().localeCompare(e.toString()))).filter(((t,e,i)=>!e||t.toString()!==i[e-1].toString()));const l=[],h=a.map((t=>t.sliceBytes)).reduce(((t,e)=>t+e),0);if(h>this.fetchSizeLimit)throw new Error(`mate data size of ${h.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);a.forEach((t=>{let 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r=t.generateTmpVariable(),s=t.generateTmpVariable();t.pushCode("var {0} = buffer.readUInt16BE(offset);",r),t.pushCode("var {0} = buffer.readUInt8(offset + 2);",s),t.pushCode("var {2} = ({0} << 8) | {1};",r,s,n),i=24}else{if(!(i<=32))throw new Error("Currently, bit field sequence longer than 4-bytes is not supported.");t.pushCode("var {0} = buffer.readUInt32BE(offset);",n),i=32}t.pushCode("offset += {0};",i/8);var o=0,a="be"===this.endian;t.bitFields.forEach((function(e){t.pushCode("{0} = {1} >> {2} & {3};",e.varName,n,a?i-o-e.options.length:o,(1< offset++);"),t.pushCode("{0} = buffer.toString('{1}', {2}, offset);",e,this.options.encoding,i)),this.options.stripNull&&t.pushCode("{0} = {0}.replace(/\\x00+$/g, '')",e)},f.prototype.generateBuffer=function(t){"eof"===this.options.readUntil?t.pushCode("{0} = buffer.slice(offset);",t.generateVariable(this.varName)):(t.pushCode("{0} = buffer.slice(offset, offset + {1});",t.generateVariable(this.varName),t.generateOption(this.options.length)),t.pushCode("offset += {0};",t.generateOption(this.options.length))),this.options.clone&&t.pushCode("{0} = Buffer.from({0});",t.generateVariable(this.varName))},f.prototype.generateArray=function(t){var e=t.generateOption(this.options.length),i=t.generateOption(this.options.lengthInBytes),n=this.options.type,r=t.generateTmpVariable(),s=t.generateVariable(this.varName),o=t.generateTmpVariable(),a=this.options.key,u="string"==typeof a;if(u?t.pushCode("{0} = {};",s):t.pushCode("{0} = [];",s),"function"==typeof this.options.readUntil?t.pushCode("do {"):"eof"===this.options.readUntil?t.pushCode("for (var {0} = 0; offset < buffer.length; {0}++) {",r):void 0!==i?t.pushCode("for (var {0} = offset; offset - {0} < {1}; ) {",r,i):t.pushCode("for (var {0} = 0; {0} < {1}; {0}++) {",r,e),"string"==typeof n)if(h[n]){var p=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",p,c+n),t.pushCode("var {0} = {1}.result; 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e=t.generateOption(this.options.tag);this.varName&&t.pushCode("{0} = {};",t.generateVariable(this.varName)),t.pushCode("switch({0}) {",e),Object.keys(this.options.choices).forEach((function(e){var i=this.options.choices[e];Number.isNaN(parseInt(e,10))?t.pushCode("case '{0}':",e):t.pushCode("case {0}:",e),this.generateChoiceCase(t,this.varName,i),t.pushCode("break;")}),this),t.pushCode("default:"),this.options.defaultChoice?this.generateChoiceCase(t,this.varName,this.options.defaultChoice):t.generateError('"Met undefined tag value " + {0} + " at choice"',e),t.pushCode("}")},f.prototype.generateNest=function(t){var e=t.generateVariable(this.varName);if(this.options.type instanceof f)this.varName&&t.pushCode("{0} = {};",e),t.pushPath(this.varName),this.options.type.generate(t),t.popPath(this.varName);else if(h[this.options.type]){var i=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",i,c+this.options.type),t.pushCode("{0} = {1}.result; offset = 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((").concat(i,"<<24) | (buffer[offset+1]<<16) | (buffer[offset+2]<<8) | buffer[offset+3]) & 0x0fffffff;\n offset += 4\n } else {\n ").concat(e," = ((").concat(i," & 0x0f)<<28) | (buffer[offset+1]<<20) | (buffer[offset+2]<<12) | (buffer[offset+3]<<4) | (buffer[offset+4] & 0x0f);\n // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);\n // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;\n offset += 5\n }\n "))},f.prototype.ltf8=function(t,e){return this.setNextParser("ltf8",t,e)},f.prototype.generateLtf8=function(t){var e=t.generateVariable(this.varName),i=t.generateTmpVariable();t.pushCode("\n var ".concat(i," = buffer[offset];\n if (").concat(i," < 0x80) {\n ").concat(e," = ").concat(i,";\n offset += 1;\n } else if (").concat(i," < 0xc0) {\n ").concat(e," = ((buffer[offset]<<8) | buffer[offset+1]) & 0x3fff;\n offset += 2;\n } else if (").concat(i," < 0xe0) {\n ").concat(e," = ((buffer[offset]<<16) | (buffer[offset+1]<<8) | buffer[offset+2]) & 0x1fffff;\n ").concat(e," = (((").concat(i," & 63) << 16) | buffer.readUInt16LE(offset + 1));\n offset += 3;\n } else if (").concat(i," < 0xf0) {\n ").concat(e," = ((buffer[offset]<<24) | (buffer[offset+1]<<16) | (buffer[offset+2]<<8) | buffer[offset+3]) & 0x0fffffff;\n offset += 4;\n } else if (").concat(i," < 0xf8) {\n ").concat(e," = (((buffer[offset] & 15) * Math.pow(2,32))) +\n (buffer[offset+1]<<24) | (buffer[offset+2]<<16 | buffer[offset+3]<<8 | buffer[offset+4])\n // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;\n offset += 5;\n } else if (").concat(i," < 0xfc) {\n ").concat(e," = ((((buffer[offset] & 7) << 8) | buffer[offset+1] )) * Math.pow(2,32) +\n (buffer[offset+2]<<24) | (buffer[offset+3]<<16 | buffer[offset+4]<<8 | buffer[offset+5])\n offset += 6;\n } else if (").concat(i," < 0xfe) {\n ").concat(e," = ((((buffer[offset] & 3) << 16) | buffer[offset+1]<<8 | buffer[offset+2])) * Math.pow(2,32) +\n (buffer[offset+3]<<24) | (buffer[offset+4]<<16 | buffer[offset+5]<<8 | buffer[offset+6])\n offset += 7;\n } else if (").concat(i," < 0xff) {\n ").concat(e," = Long.fromBytesBE(buffer.slice(offset+1,offset+8));\n if (").concat(e,".greaterThan(Number.MAX_SAFE_INTEGER) || ").concat(e,".lessThan(Number.MIN_SAFE_INTEGER))\n throw new Error('integer overflow')\n ").concat(e," = ").concat(e,".toNumber()\n offset += 8;\n } else {\n ").concat(e," = Long.fromBytesBE(buffer.slice(offset+1,offset+9));\n if (").concat(e,".greaterThan(Number.MAX_SAFE_INTEGER) || ").concat(e,".lessThan(Number.MIN_SAFE_INTEGER))\n throw new Error('integer overflow')\n ").concat(e," = ").concat(e,".toNumber()\n offset += 9;\n }\n "))},e.Parser=f},2961:(t,e)=>{function i(t){return i="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t},i(t)}var n=function(){this.code="",this.scopes=[["vars"]],this.isAsync=!1,this.bitFields=[],this.tmpVariableCount=0,this.references={}};n.prototype.generateVariable=function(t){var e=[];for(Array.prototype.push.apply(e,this.scopes[this.scopes.length-1]);/^\$parent\./.test(t);)e.pop(),t=t.replace(/^\$parent\./,"");return t&&e.push(t),e.join(".")},n.prototype.generateOption=function(t){switch(i(t)){case"number":return t.toString();case"string":return this.generateVariable(t);case"function":return"(".concat(t,").call(").concat(this.generateVariable(),", vars)");default:return}},n.prototype.generateError=function(){var t=Array.prototype.slice.call(arguments),e=n.interpolate.apply(this,t);this.isAsync?this.pushCode("return process.nextTick(function() { callback(new Error(".concat(e,"), vars); });")):this.pushCode("throw new Error(".concat(e,");"))},n.prototype.generateTmpVariable=function(){return"$tmp".concat(this.tmpVariableCount++)},n.prototype.pushCode=function(){var t=Array.prototype.slice.call(arguments);this.code+="".concat(n.interpolate.apply(this,t),"\n")},n.prototype.pushPath=function(t){t&&this.scopes[this.scopes.length-1].push(t)},n.prototype.popPath=function(t){t&&this.scopes[this.scopes.length-1].pop()},n.prototype.pushScope=function(t){this.scopes.push([t])},n.prototype.popScope=function(){this.scopes.pop()},n.prototype.addReference=function(t){this.references[t]||(this.references[t]={resolved:!1,requested:!1})},n.prototype.markResolved=function(t){this.references[t].resolved=!0},n.prototype.markRequested=function(t){t.forEach(function(t){this.references[t].requested=!0}.bind(this))},n.prototype.getUnresolvedReferences=function(){var t=this.references;return Object.keys(this.references).filter((function(e){return!t[e].resolved&&!t[e].requested}))},n.interpolate=function(t){var e=t.match(/{\d+}/g),i=Array.prototype.slice.call(arguments,1);return e&&e.forEach((function(e){var n=parseInt(e.substr(1,e.length-2),10);t=t.replace(e,i[n].toString())})),t},e._=n},22:t=>{t.exports.runInThisContext=function(t){return new Function("code","return eval(code);").call(globalThis,t)}},445:(t,e,i)=>{const n=i(7381),r=i(9260),s=i(576),o=i(4693),a=128;t.exports=class{decode(t){return this.stream=new r(t),this.decodeStream(this.stream)}decodeStream(t,e=0){var i=this.stream.ReadByte();16&i||(e=this.stream.ReadUint7());var n,r=e,s=1&i;if(8&i)return this.decodeStripe(this.stream,e);if(i&a&&([n,r]=this.decodePackMeta(this.stream)),32&i)var o=this.decodeCat(this.stream,r);else o=4&i?this.decodeExt(this.stream,r):64&i?s?this.decodeRLE1(this.stream,r):this.decodeRLE0(this.stream,r):s?this.decode1(this.stream,r):this.decode0(this.stream,r);return i&a&&(o=this.decodePack(o,n,e)),o}encode(t,e){if(this.stream=new r("",0,1.1*t.length+100),this.stream.WriteByte(e),16&e||this.stream.WriteUint7(t.length),8&e)return Buffer.concat([this.stream.buf.slice(0,this.stream.pos),this.encodeStripe(this.stream,t,e>>8)]);var i,n=1&e,s=t.length;return e&a&&([i,t,s]=this.encodePack(t)),e&a&&this.stream.WriteStream(i),64&e?n?this.encodeRLE1(t,s,this.stream):this.encodeRLE0(t,s,this.stream):n?this.encode1(t,s,this.stream):this.encode0(t,s,this.stream)}decode0(t,e){var i=new Buffer.allocUnsafe(e),r=t.ReadByte();0==r&&(r=256);var o=new s(r),a=new n(t);a.RangeStartDecode(t);for(var l=0;l=3?3:c;for(l[u].ModelEncode(i,h,d),c-=d,u=256;3==d;)d=c>=3?3:c,l[u].ModelEncode(i,h,d),u=257,c-=d}return h.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeRLE1(t,e){var i=new Buffer.allocUnsafe(e),r=t.ReadByte();0==r&&(r=256);for(var o=new Array(r),a=0;a=3?3:u;for(l[d].ModelEncode(i,h,f),u-=f,d=256;3==f;)f=u>=3?3:u,l[d].ModelEncode(i,h,f),d=257,u-=f}return h.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodePackMeta(t){this.nsym=t.ReadByte();for(var e=new Array(this.nsym),i=0;i>=1}}else if(this.nsym<=4)for(r=0,s=0;r>=2;else{if(!(this.nsym<=16))return t;for(r=0,s=0;r>=4}return n}packMeta(t){for(var e=new r("",0,1024),i=new Array(256),n=0;no),n[o]=new Array(s[o]);for(var a=0,l=0;ls),o[s]=this.decodeStream(t,r[s]);var a=new Buffer.allocUnsafe(e);for(s=0;s{t.exports=class{constructor(t){this.low=0,this.range=4294967295,this.code=0,this.FFnum=0,this.carry=0,this.cache=0}RangeStartDecode(t){for(var e=0;e<5;e++)this.code=(this.code<<8)+t.ReadByte();this.code&=4294967295,this.code>>>=0}RangeGetFrequency(t){return this.range=Math.floor(this.range/t),Math.floor(this.code/this.range)}RangeDecode(t,e,i,n){for(this.code-=e*this.range,this.range*=i;this.range<1<<24;)this.range*=256,this.code=256*this.code+t.ReadByte()}RangeShiftLow(t){if(this.low<4278190080|this.carry){for(t.WriteByte(this.cache+this.carry);this.FFnum;)t.WriteByte(this.carry-1),this.FFnum--;this.cache=this.low>>>24,this.carry=0}else this.FFnum++;this.low<<=8,this.low>>>=0}RangeEncode(t,e,i,n){var r=this.low;for(this.range=Math.floor(this.range/n),this.low+=e*this.range,this.low>>>=0,this.range*=i,this.low{t.exports=class{constructor(t=256){this.total_freq=t,this.max_sym=t-1,this.S=new Array,this.F=new Array;for(var e=0;e<=this.max_sym;e++)this.S[e]=e,this.F[e]=1}ModelDecode(t,e){for(var i=e.RangeGetFrequency(this.total_freq),n=0,r=0;n+this.F[r]<=i;)n+=this.F[r++];e.RangeDecode(t,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise();var s=this.S[r];if(r>0&&this.F[r]>this.F[r-1]){var o=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=o,o=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=o}return s}ModelRenormalise(){this.total_freq=0;for(var t=0;t<=this.max_sym;t++)this.F[t]-=Math.floor(this.F[t]/2),this.total_freq+=this.F[t]}ModelEncode(t,e,i){for(var n=0,r=0;this.S[r]!=i;r++)n+=this.F[r];if(e.RangeEncode(t,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise(),i=this.S[r],r>0&&this.F[r]>this.F[r-1]){var s=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=s,s=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=s}}}},5260:(t,e,i)=>{const n=i(9260),r=i(576),s=i(7381);function o(t,e,i){for(var n=0,r=0,s=-1,o=new Array(1024);r>4,e.qshift=15&i,i=t.ReadByte(),e.qloc=i>>4,e.sloc=15&i,i=t.ReadByte(),e.ploc=i>>4,e.dloc=15&i,e.qmap=new Array(256),16&e.pflags)for(var n=0;n0&&128&e.pflags)o(t,e.qtab,256);else for(n=0;n<256;n++)e.qtab[n]=n;return e.ptab=new Array(1024),32&e.pflags&&o(t,e.ptab,1024),e.dtab=new Array(256),64&e.pflags&&o(t,e.dtab,256),e}function h(t,e,i,n,r,s){i.max_sel>0?r.s=n.sel.ModelDecode(t,e):r.s=0,r.x=i.stab[r.s];var o=i.params[r.x];if(o.fixed_len>=0){var a=n.len[0].ModelDecode(t,e);a|=n.len[1].ModelDecode(t,e)<<8,a|=n.len[2].ModelDecode(t,e)<<16,a|=n.len[3].ModelDecode(t,e)<<24,o.fixed_len>0&&(o.fixed_len=-a)}else a=-o.fixed_len;r.len=a,i.do_rev&&(s[r.rec]=n.rev.ModelDecode(t,e)),r.is_dup=0,2&o.pflags&&n.dup.ModelDecode(t,e)&&(r.is_dup=1),r.p=a,r.delta=0,r.qctx=0,r.prevq=0,r.rec++}function c(t,e,i){for(var n=0,r=0,s=new Array(2*i),o=0;n1?i.nparam-1:0,s=new Array(256);if(2&i)r=t.ReadByte(),o(t,s,256);else{for(var a=0;a0&&(e.sel=new r(t.max_sel+1)),e}(n),f=new s(t);f.RangeStartDecode(t);for(var p=new Buffer.allocUnsafe(i),g={qctx:0,prevq:0,delta:0,p:0,s:0,x:0,len:0,is_dup:0,rec:0},m=0;m0&&d.dup.ModelDecode(t,f)){for(var b=0;b4),qshift:u,qloc:7,pbits:7,pshift:e[0]>128?1:0,ploc:0,dbits:u>4?0:1,dshift:3,dloc:15,sbits:0,sloc:15,do_stab:0,context:0,max_sym:l,nsym:a,do_qmap:d,do_dedup:0,fixed_len:1==e.length?1:0,do_sel:0,do_rev:0,do_pos:1,do_delta:u<=4?1:0,do_qtab:0,qbits:8+(u>4)-(0==o),sbits:1,sloc:15-(u<=4),do_stab:1,do_sel:1}]}(t,e,i,o),p=function(t,e,i,n,r,s,o){for(var a=[0,1,1,1,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7],l=0;l1?1:0)|(e[0].do_stab?2:0);if(t.WriteByte(h),1&h&&t.WriteByte(e.length),2&h){var u=1<0&&u--,t.WriteByte(u),c(t,o,256)}for(var d=0;d0){for(l=0;l<256;l++)n[d][l]=l;e[d].do_qtab&&c(t,n[d],256)}if(e[d].pbits>0){for(l=0;l<1024;l++)r[d][l]=Math.min((1<>e[d].pshift);c(t,r[d],1024)}if(e[d].dbits>0){for(l=0;l<256;l++)a[l]>(1<>e[d].dshift)];c(t,s[d],256)}}return t}(p,f,o,a,l,h,u);return function(t,e,i,n,o,a,l,h,c,u){var d=1<0&&d--;for(var f=e.length,p=0,g=0;g0&&v.ModelEncode(t,w,x);var k=u[x],S=i[Math.min(i.length-1,_++)];o[k].fixed_len?o[k].fixed_len>0&&(y[0].ModelEncode(t,w,255&S),y[1].ModelEncode(t,w,S>>8&255),y[2].ModelEncode(t,w,S>>16&255),y[3].ModelEncode(t,w,S>>24&255),o[k].fixed_len=-1):(y[0].ModelEncode(t,w,255&S),y[1].ModelEncode(t,w,S>>8&255),y[2].ModelEncode(t,w,S>>16&255),y[3].ModelEncode(t,w,S>>24&255)),o[k].do_dedup&&process.exit(1),g=S;var C=0,A=o[k].context,T=0,I=0}var E=e[b++],M=a[k][E];m[A].ModelEncode(t,w,M),T=(T<0&&(A+=h[k][Math.min(g,1023)]<0&&(A+=c[k][Math.min(C,255)]<{var n=i(4459),r=i(594),s=i(445),o=i(5260),a=i(2881);t.exports={r4x8_uncompress:function(t,e){n.decode(t).copy(e,0,0)},r4x16_uncompress:function(t,e){r.decode(t).copy(e,0,0)},arith_uncompress:function(t,e){s.decode(t).copy(e,0,0)},fqzcomp_uncompress:function(t,e){var i=new Array;o.decode(t,i).copy(e,0,0)},tok3_uncompress:function(t,e){var i=a.decode(t,0,"\0");Buffer.from(i,"binary").copy(e,0,0)}}},9260:t=>{t.exports=class{constructor(t,e=0,i=0){0!=i?(this.buf=Buffer.allocUnsafe(i),this.length=i):(this.buf=t,this.length=t.length),this.pos=e}EOF(){return this.pos>=this.length}ReadData(t){var e=this.buf.slice(this.pos,this.pos+t);return this.pos+=t,e}ReadByte(){const t=this.buf[this.pos];return this.pos++,t}ReadChar(){const t=this.buf[this.pos];return this.pos++,String.fromCharCode(t)}ReadUint16(){return this.ReadByte()|this.ReadByte()<<8}ReadUint32(){const t=this.buf.readInt32LE(this.pos);return this.pos+=4,t}ReadString(){var t="";do{var e=this.buf[this.pos++];e&&(t+=String.fromCharCode(e))}while(e);return t}ReadUint7(){var t=0;do{var e=this.ReadByte();t=t<<7|127&e}while(128&e);return t}ReadITF8(){var t=this.buf[this.pos];return this.pos++,t>=240?(t=(15&t)<<28,t+=(this.buf[this.pos+0]<<20)+(this.buf[this.pos+1]<<12)+(this.buf[this.pos+2]<<4)+(this.buf[this.pos+3]>>4),this.pos+=4):t>=224?(t=(15&t)<<24,t+=(this.buf[this.pos+0]<<16)+(this.buf[this.pos+1]<<8)+(this.buf[this.pos+2]<<0),this.pos+=3):t>=192?(t=(31&t)<<16,t+=(this.buf[this.pos+0]<<8)+(this.buf[this.pos+1]<<0),this.pos+=2):t>=128&&(t=(63&t)<<8,t+=this.buf[this.pos],this.pos++),t}WriteByte(t){this.buf[this.pos++]=t}WriteChar(t){this.buf[this.pos++]=t.charCodeAt(0)}WriteString(t){for(var e=0;e>8&255)}WriteUint32(t){this.buf.writeInt32LE(t,this.pos),this.pos+=4}WriteUint7(t){var e=0,i=t;do{e+=7,i>>=7}while(i>0);do{e-=7,this.WriteByte((t>>e&127)+((e>0)<<7))}while(e>0)}WriteITF8(t){t<0&&(t=1+t),t<=127?this.buf[this.pos++]=t:t<=16383?(this.buf[this.pos++]=128|Math.floor(t/256),this.buf[this.pos++]=255&t):t<131071?(this.buf[this.pos++]=192|Math.floor(t/65536),this.buf[this.pos++]=255&Math.floor(t/256),this.buf[this.pos++]=255&t):t<268435455?(this.buf[this.pos++]=224|Math.floor(t/16777216),this.buf[this.pos++]=255&Math.floor(t/65536),this.buf[this.pos++]=255&Math.floor(t/256),this.buf[this.pos++]=255&t):(this.buf[this.pos++]=240|Math.floor(t/268435456),this.buf[this.pos++]=255&Math.floor(t/1048576),this.buf[this.pos++]=255&Math.floor(t/4096),this.buf[this.pos++]=255&Math.floor(t/4),this.buf[this.pos++]=15&t)}WriteByteNeg(t){this.buf[--this.pos]=t}}},4459:(t,e,i)=>{const n=i(9260);function r(t){return 4095&t}function s(t,e){for(var i=0;e>=t[i+1];)i++;return i}function o(t){for(var e=new Array(4096),i=0,n=0;n<4096;n++){for(;n>=t[i+1];)i++;e[n]=i}return e}function a(t,e,i){return i*(t>>12)+(4095&t)-e}function l(t,e){for(;e<1<<23;)e=(e<<8)+t.ReadByte();return e}function h(t,e){e.WriteByteNeg(t>>24&255),e.WriteByteNeg(t>>16&255),e.WriteByteNeg(t>>8&255),e.WriteByteNeg(t>>0&255)}function c(t,e,i,n,r){return t=function(t,e,i,n){for(var r=(1<<23>>n<<8)*i;t>=r;)e.WriteByteNeg(255&t),t>>=8;return t}(t,e,n,r),(Math.floor(t/n)<0?(o--,r++):(r=t.ReadByte())==s+1&&(o=t.ReadByte()),s=r}while(0!=r);for(i[0]=0,n=0;n<=255;n++)i[n+1]=i[n]+e[n]}function d(t){for(var e=0,i=0;i<256;i++)e+=t[i];const n=4096;var r=n/e;do{var s=0,o=0,a=0;for(e=0,i=0;i<256;i++)0!=t[i]&&(s2?t[o]-=e-n:e!=n&&(r*=.99,a=1)}while(a)}function f(t,e){for(var i=0,n=0;n<256;n++)if(e[n]){if(i>0)i--;else if(t.WriteByte(n),n>0&&e[n-1]>0){for(i=n+1;i<256&&e[i];i++);i-=n+1,t.WriteByte(i)}t.WriteITF8(e[n])}t.WriteByte(0)}t.exports={decode:function(t){var e=new n(t),i=e.ReadByte(),h=(e.ReadUint32(),e.ReadUint32());return 0==i?function(t,e){var i=new Array(256),n=new Array(256);u(t,i,n);for(var 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n.Buf32(32),e=0;e<144;)t.lens[e++]=8;for(;e<256;)t.lens[e++]=9;for(;e<280;)t.lens[e++]=7;for(;e<288;)t.lens[e++]=8;for(a(1,t.lens,0,288,b,0,t.work,{bits:9}),e=0;e<32;)t.lens[e++]=5;a(2,t.lens,0,32,y,0,t.work,{bits:5}),v=!1}t.lencode=b,t.lenbits=9,t.distcode=y,t.distbits=5}function _(t,e,i,r){var s,o=t.state;return null===o.window&&(o.wsize=1<=o.wsize?(n.arraySet(o.window,e,i-o.wsize,o.wsize,0),o.wnext=0,o.whave=o.wsize):((s=o.wsize-o.wnext)>r&&(s=r),n.arraySet(o.window,e,i-r,s,o.wnext),(r-=s)?(n.arraySet(o.window,e,i-r,r,0),o.wnext=r,o.whave=o.wsize):(o.wnext+=s,o.wnext===o.wsize&&(o.wnext=0),o.whave>>8&255,i.check=s(i.check,P,2,0),y=0,v=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&y)<<8)+(y>>8))%31){t.msg="incorrect header check",i.mode=c;break}if(8!=(15&y)){t.msg="unknown compression method",i.mode=c;break}if(v-=4,B=8+(15&(y>>>=4)),0===i.wbits)i.wbits=B;else if(B>i.wbits){t.msg="invalid window size",i.mode=c;break}i.dmax=1<>8&1),512&i.flags&&(P[0]=255&y,P[1]=y>>>8&255,i.check=s(i.check,P,2,0)),y=0,v=0,i.mode=3;case 3:for(;v<32;){if(0===m)break t;m--,y+=d[p++]<>>8&255,P[2]=y>>>16&255,P[3]=y>>>24&255,i.check=s(i.check,P,4,0)),y=0,v=0,i.mode=4;case 4:for(;v<16;){if(0===m)break t;m--,y+=d[p++]<>8),512&i.flags&&(P[0]=255&y,P[1]=y>>>8&255,i.check=s(i.check,P,2,0)),y=0,v=0,i.mode=5;case 5:if(1024&i.flags){for(;v<16;){if(0===m)break t;m--,y+=d[p++]<>>8&255,i.check=s(i.check,P,2,0)),y=0,v=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((S=i.length)>m&&(S=m),S&&(i.head&&(B=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,d,p,S,B)),512&i.flags&&(i.check=s(i.check,d,S,p)),m-=S,p+=S,i.length-=S),i.length))break t;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===m)break t;S=0;do{B=d[p+S++],i.head&&B&&i.length<65536&&(i.head.name+=String.fromCharCode(B))}while(B&&S>9&1,i.head.done=!0),t.adler=i.check=0,i.mode=h;break;case 10:for(;v<32;){if(0===m)break t;m--,y+=d[p++]<>>=7&v,v-=7&v,i.mode=27;break}for(;v<3;){if(0===m)break t;m--,y+=d[p++]<>>=1)){case 0:i.mode=14;break;case 1:if(w(i),i.mode=20,6===e){y>>>=2,v-=2;break t}break;case 2:i.mode=17;break;case 3:t.msg="invalid block type",i.mode=c}y>>>=2,v-=2;break;case 14:for(y>>>=7&v,v-=7&v;v<32;){if(0===m)break t;m--,y+=d[p++]<>>16^65535)){t.msg="invalid stored block lengths",i.mode=c;break}if(i.length=65535&y,y=0,v=0,i.mode=15,6===e)break t;case 15:i.mode=16;case 16:if(S=i.length){if(S>m&&(S=m),S>b&&(S=b),0===S)break t;n.arraySet(f,d,p,S,g),m-=S,p+=S,b-=S,g+=S,i.length-=S;break}i.mode=h;break;case 17:for(;v<14;){if(0===m)break t;m--,y+=d[p++]<>>=5,v-=5,i.ndist=1+(31&y),y>>>=5,v-=5,i.ncode=4+(15&y),y>>>=4,v-=4,i.nlen>286||i.ndist>30){t.msg="too many length or distance symbols",i.mode=c;break}i.have=0,i.mode=18;case 18:for(;i.have>>=3,v-=3}for(;i.have<19;)i.lens[z[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,F={bits:i.lenbits},N=a(0,i.lens,0,19,i.lencode,0,i.work,F),i.lenbits=F.bits,N){t.msg="invalid code lengths set",i.mode=c;break}i.have=0,i.mode=19;case 19:for(;i.have>>16&255,E=65535&D,!((T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>>=T,v-=T,i.lens[i.have++]=E;else{if(16===E){for(O=T+2;v>>=T,v-=T,0===i.have){t.msg="invalid bit length repeat",i.mode=c;break}B=i.lens[i.have-1],S=3+(3&y),y>>>=2,v-=2}else if(17===E){for(O=T+3;v>>=T)),y>>>=3,v-=3}else{for(O=T+7;v>>=T)),y>>>=7,v-=7}if(i.have+S>i.nlen+i.ndist){t.msg="invalid bit length repeat",i.mode=c;break}for(;S--;)i.lens[i.have++]=B}}if(i.mode===c)break;if(0===i.lens[256]){t.msg="invalid code -- missing end-of-block",i.mode=c;break}if(i.lenbits=9,F={bits:i.lenbits},N=a(1,i.lens,0,i.nlen,i.lencode,0,i.work,F),i.lenbits=F.bits,N){t.msg="invalid literal/lengths set",i.mode=c;break}if(i.distbits=6,i.distcode=i.distdyn,F={bits:i.distbits},N=a(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,F),i.distbits=F.bits,N){t.msg="invalid distances set",i.mode=c;break}if(i.mode=20,6===e)break t;case 20:i.mode=21;case 21:if(m>=6&&b>=258){t.next_out=g,t.avail_out=b,t.next_in=p,t.avail_in=m,i.hold=y,i.bits=v,o(t,k),g=t.next_out,f=t.output,b=t.avail_out,p=t.next_in,d=t.input,m=t.avail_in,y=i.hold,v=i.bits,i.mode===h&&(i.back=-1);break}for(i.back=0;I=(D=i.lencode[y&(1<>>16&255,E=65535&D,!((T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>M)])>>>16&255,E=65535&D,!(M+(T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>>=M,v-=M,i.back+=M}if(y>>>=T,v-=T,i.back+=T,i.length=E,0===I){i.mode=26;break}if(32&I){i.back=-1,i.mode=h;break}if(64&I){t.msg="invalid literal/length code",i.mode=c;break}i.extra=15&I,i.mode=22;case 22:if(i.extra){for(O=i.extra;v>>=i.extra,v-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;I=(D=i.distcode[y&(1<>>16&255,E=65535&D,!((T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>M)])>>>16&255,E=65535&D,!(M+(T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>>=M,v-=M,i.back+=M}if(y>>>=T,v-=T,i.back+=T,64&I){t.msg="invalid distance code",i.mode=c;break}i.offset=E,i.extra=15&I,i.mode=24;case 24:if(i.extra){for(O=i.extra;v>>=i.extra,v-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){t.msg="invalid distance too far back",i.mode=c;break}i.mode=25;case 25:if(0===b)break t;if(S=k-b,i.offset>S){if((S=i.offset-S)>i.whave&&i.sane){t.msg="invalid distance too far back",i.mode=c;break}S>i.wnext?(S-=i.wnext,C=i.wsize-S):C=i.wnext-S,S>i.length&&(S=i.length),A=i.window}else A=f,C=g-i.offset,S=i.length;S>b&&(S=b),b-=S,i.length-=S;do{f[g++]=A[C++]}while(--S);0===i.length&&(i.mode=21);break;case 26:if(0===b)break t;f[g++]=i.length,b--,i.mode=21;break;case 27:if(i.wrap){for(;v<32;){if(0===m)break t;m--,y|=d[p++]<{var n=i(4236),r=[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],s=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],o=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],a=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64];t.exports=function(t,e,i,l,h,c,u,d){var f,p,g,m,b,y,v,w,_,x=d.bits,k=0,S=0,C=0,A=0,T=0,I=0,E=0,M=0,R=0,L=0,B=null,N=0,F=new n.Buf16(16),O=new n.Buf16(16),D=null,P=0;for(k=0;k<=15;k++)F[k]=0;for(S=0;S=1&&0===F[A];A--);if(T>A&&(T=A),0===A)return h[c++]=20971520,h[c++]=20971520,d.bits=1,0;for(C=1;C0&&(0===t||1!==A))return-1;for(O[1]=0,k=1;k<15;k++)O[k+1]=O[k]+F[k];for(S=0;S852||2===t&&R>592)return 1;for(;;){v=k-E,u[S]y?(w=D[P+u[S]],_=B[N+u[S]]):(w=96,_=0),f=1<>E)+(p-=f)]=v<<24|w<<16|_|0}while(0!==p);for(f=1<>=1;if(0!==f?(L&=f-1,L+=f):L=0,S++,0==--F[k]){if(k===A)break;k=e[i+u[S]]}if(k>T&&(L&m)!==g){for(0===E&&(E=T),b+=C,M=1<<(I=k-E);I+E852||2===t&&R>592)return 1;h[g=L&m]=T<<24|I<<16|b-c|0}}return 0!==L&&(h[b+L]=k-E<<24|64<<16|0),d.bits=T,0}},8898:t=>{t.exports={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"}},342:(t,e,i)=>{var n=i(4236);function r(t){for(var e=t.length;--e>=0;)t[e]=0}var s=[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],o=[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],a=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],l=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],h=new Array(576);r(h);var c=new Array(60);r(c);var u=new Array(512);r(u);var d=new Array(256);r(d);var f=new Array(29);r(f);var p,g,m,b=new Array(30);function y(t,e,i,n,r){this.static_tree=t,this.extra_bits=e,this.extra_base=i,this.elems=n,this.max_length=r,this.has_stree=t&&t.length}function v(t,e){this.dyn_tree=t,this.max_code=0,this.stat_desc=e}function w(t){return t<256?u[t]:u[256+(t>>>7)]}function _(t,e){t.pending_buf[t.pending++]=255&e,t.pending_buf[t.pending++]=e>>>8&255}function x(t,e,i){t.bi_valid>16-i?(t.bi_buf|=e<>16-t.bi_valid,t.bi_valid+=i-16):(t.bi_buf|=e<>>=1,i<<=1}while(--e>0);return i>>>1}function C(t,e,i){var n,r,s=new Array(16),o=0;for(n=1;n<=15;n++)s[n]=o=o+i[n-1]<<1;for(r=0;r<=e;r++){var a=t[2*r+1];0!==a&&(t[2*r]=S(s[a]++,a))}}function A(t){var e;for(e=0;e<286;e++)t.dyn_ltree[2*e]=0;for(e=0;e<30;e++)t.dyn_dtree[2*e]=0;for(e=0;e<19;e++)t.bl_tree[2*e]=0;t.dyn_ltree[512]=1,t.opt_len=t.static_len=0,t.last_lit=t.matches=0}function T(t){t.bi_valid>8?_(t,t.bi_buf):t.bi_valid>0&&(t.pending_buf[t.pending++]=t.bi_buf),t.bi_buf=0,t.bi_valid=0}function I(t,e,i,n){var r=2*e,s=2*i;return t[r]>1;i>=1;i--)E(t,s,i);r=l;do{i=t.heap[1],t.heap[1]=t.heap[t.heap_len--],E(t,s,1),n=t.heap[1],t.heap[--t.heap_max]=i,t.heap[--t.heap_max]=n,s[2*r]=s[2*i]+s[2*n],t.depth[r]=(t.depth[i]>=t.depth[n]?t.depth[i]:t.depth[n])+1,s[2*i+1]=s[2*n+1]=r,t.heap[1]=r++,E(t,s,1)}while(t.heap_len>=2);t.heap[--t.heap_max]=t.heap[1],function(t,e){var i,n,r,s,o,a,l=e.dyn_tree,h=e.max_code,c=e.stat_desc.static_tree,u=e.stat_desc.has_stree,d=e.stat_desc.extra_bits,f=e.stat_desc.extra_base,p=e.stat_desc.max_length,g=0;for(s=0;s<=15;s++)t.bl_count[s]=0;for(l[2*t.heap[t.heap_max]+1]=0,i=t.heap_max+1;i<573;i++)(s=l[2*l[2*(n=t.heap[i])+1]+1]+1)>p&&(s=p,g++),l[2*n+1]=s,n>h||(t.bl_count[s]++,o=0,n>=f&&(o=d[n-f]),a=l[2*n],t.opt_len+=a*(s+o),u&&(t.static_len+=a*(c[2*n+1]+o)));if(0!==g){do{for(s=p-1;0===t.bl_count[s];)s--;t.bl_count[s]--,t.bl_count[s+1]+=2,t.bl_count[p]--,g-=2}while(g>0);for(s=p;0!==s;s--)for(n=t.bl_count[s];0!==n;)(r=t.heap[--i])>h||(l[2*r+1]!==s&&(t.opt_len+=(s-l[2*r+1])*l[2*r],l[2*r+1]=s),n--)}}(t,e),C(s,h,t.bl_count)}function L(t,e,i){var n,r,s=-1,o=e[1],a=0,l=7,h=4;for(0===o&&(l=138,h=3),e[2*(i+1)+1]=65535,n=0;n<=i;n++)r=o,o=e[2*(n+1)+1],++a>=7;n<30;n++)for(b[n]=r<<7,t=0;t<1<0?(2===t.strm.data_type&&(t.strm.data_type=function(t){var e,i=4093624447;for(e=0;e<=31;e++,i>>>=1)if(1&i&&0!==t.dyn_ltree[2*e])return 0;if(0!==t.dyn_ltree[18]||0!==t.dyn_ltree[20]||0!==t.dyn_ltree[26])return 1;for(e=32;e<256;e++)if(0!==t.dyn_ltree[2*e])return 1;return 0}(t)),R(t,t.l_desc),R(t,t.d_desc),o=function(t){var e;for(L(t,t.dyn_ltree,t.l_desc.max_code),L(t,t.dyn_dtree,t.d_desc.max_code),R(t,t.bl_desc),e=18;e>=3&&0===t.bl_tree[2*l[e]+1];e--);return t.opt_len+=3*(e+1)+5+5+4,e}(t),r=t.opt_len+3+7>>>3,(s=t.static_len+3+7>>>3)<=r&&(r=s)):r=s=i+5,i+4<=r&&-1!==e?F(t,e,i,n):4===t.strategy||s===r?(x(t,2+(n?1:0),3),M(t,h,c)):(x(t,4+(n?1:0),3),function(t,e,i,n){var 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e of this.oldCache.keys())this.cache.has(e)||t++;return this._size+t}}var Vu={ALIGNMENT_MATCH:"M",INSERT:"I",DELETE:"D",SKIP:"N",CLIP_SOFT:"S",CLIP_HARD:"H",PAD:"P",SEQUENCE_MATCH:"=",SEQUENCE_MISMATCH:"X"};const Hu=function(t,e){this.config=t,this.genome=e,this.url=t.url,this.filter=new wu(t.filter),this.readGroupSetIds=t.readGroupSetIds,this.authKey=t.authKey,this.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,this.samplingDepth=void 0===t.samplingDepth?1e3:t.samplingDepth,t.viewAsPairs?this.pairsSupported=!0:this.pairsSupported=void 0===t.pairsSupported||t.pairsSupported};Hu.prototype.readAlignments=function(t,e,i){const n=this.genome,r=this;return(r.chrAliasTable?Promise.resolve(r.chrAliasTable):r.readMetadata().then((function(t){if(r.chrAliasTable={},n&&t.readGroups&&t.readGroups.length>0){var e=t.readGroups[0].referenceSetId;return e?oc({url:r.url+"/references/search",body:{referenceSetId:e},decode:function(t){return 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.picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(ad),od.StyleElement=ad;const hd={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};class cd{constructor(t){this.tracks=[],this.chordSets=[]}addChordSet(t){this.chordSets=this.chordSets.filter((e=>e.name!==t.name)),this.chordSets.push(t);let e=this.tracks.find((e=>t.trackName===e.name));e&&(e.chordSets=e.chordSets.filter((e=>e.name!==t.name)),e.chordSets.push(t)),e||(e=new ud(t),this.tracks.push(e))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(t){return this.tracks.find((e=>t===e.name))}getChordSet(t){return this.chordSets.find((e=>t===e.name))}}class ud{constructor(t){this.name=t.trackName,this.color=t.trackColor,this.visible=!0,this.chordSets=[t],this.id=("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const t=[];for(let e of this.chordSets)for(let i of e.chords)t.push(i);return t}}const dd=Math.exp(5);class fd{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(t,e){if(e=e||{},this.config=e,fd.isInstalled()){this.parent=t,this.groupByTrack=!0===e.groupByTrack,this.chordManager=new cd(e);const i=document.createElement("div");i.className="igv-circview-container",t.appendChild(i),this.createControls(i),this.resetControlPanel();const n=document.createElement("div");n.className="igv-circview-circular-genome-view",i.appendChild(n),this.container=n,e.assembly&&this.setAssembly(e.assembly),this.width=e.width||500,this.height=e.height||500,this.setSize(this.width,this.height)}else console.error("JBrowse circular view is not installed")}createControls(t){const e=document.createElement("div");e.className="igv-circview-toolbar",t.appendChild(e),this.toolbar=e;const i=document.createElement("div");i.className="igv-circview-track-panel",t.appendChild(i),this.controlPanel=i,this.controlPanel.style.display="none";const n=document.createElement("div");n.className="igv-circview-toolbar-button-container",this.toolbar.appendChild(n),this.showControlsButton=document.createElement("div"),this.showControlsButton.className="igv-circview-button",n.appendChild(this.showControlsButton),this.showControlsButton.innerText="none"===this.controlPanel.style.display?"Show Controls":"Hide Controls",this.showControlsButton.addEventListener("click",(t=>{this.controlPanel.querySelectorAll("div").length>0&&("none"===this.controlPanel.style.display?(this.controlPanel.style.display="flex",t.target.innerText="Hide Controls"):(this.controlPanel.style.display="none",t.target.innerText="Show Controls"))}));let r=document.createElement("div");r.className="igv-circview-button",n.appendChild(r),r.innerText="Clear All",r.addEventListener("click",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(r=document.createElement("div"),r.className="igv-circview-button",n.appendChild(r),r.innerText="Close",r.addEventListener("click",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML="",this.controlPanel.appendChild(this.createGroupByCB());const t=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let e of t)this.addToControlPanel(e)}createGroupByCB(){const t=document.createElement("input");t.type="checkbox",t.id="groupByCB",t.style.width="1.4em",t.style.height="1.4em",t.checked=this.groupByTrack,t.onclick=t=>{this.groupByTrack=t.target.checked,this.resetControlPanel(),this.render()};const e=document.createElement("label");e.for="groupByCB",e.innerText="Group by track",e.style.color="black",e.style.paddingLeft="10px";const i=document.createElement("div");return i.style.width="100%",i.style.paddingTop="5px",i.style.paddingBottom="5px",i.style.background="rgb(216, 230, 234)",i.appendChild(t),i.appendChild(e),i}addToControlPanel(t){const e=document.createElement("div");this.controlPanel.appendChild(e);const i=document.createElement("div");i.className="igv-circview-button",e.appendChild(i),i.innerText=!0===t.visible?"Hide":"Show",i.addEventListener("click",(e=>{!0===t.visible?(this.hideChordSet(t.name),e.target.innerText="Show"):(this.showChordSet(t.name),e.target.innerText="Hide")}));const n=document.createElement("input"),r=t=>200*Math.log(t*dd),s=document.createElement("div");s.className="igv-circview-button",s.innerHTML="    ",e.appendChild(s),s.style.backgroundColor=pd(t.color,1);const o={parent:s,popup:"right",editorFormat:"rgb",color:t.color,onChange:({rgbaString:e})=>{s.style.backgroundColor=pd(e,1),this.setColor(t.name,e),n.value=r(gd(t.color))}},a=new od(o);n.setAttribute("title","Adjust transparency of arcs"),n.type="range",n.style.width="100px",n.style.marginRight="10px",n.setAttribute("class","range"),n.setAttribute("min","0"),n.setAttribute("max","1000"),n.value=r(gd(t.color)),n.oninput=()=>{const e=(i=n.value,Math.exp(i/200)/dd);var i;this.setColor(t.name,pd(t.color,e)),a.setColor(t.color)},e.appendChild(n);const l=document.createElement("div");l.style.color="black",e.appendChild(l),l.innerText=l.title=t.name}setAssembly(t){const e=this.genomeId||yd();if(this.genomeId===e)return;this.chordManager.clearChords(),this.genomeId=e,this.chrNames=new Set(t.chromosomes.map((t=>md(t.name))));const i=[],n=[];for(let e of t.chromosomes){const t=md(e.name);n.push(e.color||ld(t)),i.push({refName:t,uniqueId:t,start:0,end:e.bpLength})}this.assembly={name:t.name,sequence:{trackId:e,type:"ReferenceSequenceTrack",adapter:{type:"FromConfigSequenceAdapter",features:i}},refNameColors:n},this.render()}addChords(t,e={}){const i=e.name||e.track||"*",n=i.split(" ")[0].replaceAll("%20"," "),r={name:i.replaceAll("%20"," "),trackName:n,chords:t,color:e.color||"black",trackColor:e.trackColor||e.color||"black",visible:!0,id:e.id||yd()};this.chordManager.addChordSet(r),this.resetControlPanel(),this.render()}setSize(t,e){if(e=e||t,this.width=t,this.height=e,this.viewState){const i=this.viewState.session.view;i.setWidth(t),i.setHeight(e),i.setBpPerPx(i.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display="block"}hide(){this.parent.style.display="none"}get visible(){return"none"!==this.parent.style.display}set visible(t){this.parent.style.display=t?"block":"none"}hideChordSet(t){let e=this.getChordSet(t);e?(e.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(t){let e=this.getChordSet(t);e?(e.visible=!0,this.render()):console.warn(`No track with name: ${t}`)}deleteTrack(t){let e=this.tracks.findIndex((e=>t===e.name));e>=0&&this.tracks.splice(e,1),this.render()}getChordSet(t){return this.groupByTrack?this.chordManager.getTrack(t):this.chordManager.getChordSet(t)}setColor(t,e){const i=this.getChordSet(t);if(i){i.color=e;const t=i.id;for(let i of this.viewState.config.tracks)if(t===i.trackId){i.displays[0].renderer.strokeColor.set(e);break}}}render(){const{createViewState:t,JBrowseCircularGenomeView:e}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const i=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((t=>t.visible)),n=[],r=[];for(let t of i)n.push({trackId:t.id,name:t.name,assemblyNames:["forIGV"],type:"VariantTrack",adapter:{type:"FromConfigAdapter",features:t.chords}}),r.push(t.color);this.viewState=t({assembly:this.assembly,tracks:n});for(let t=0;t div {\n margin: 4px;\n}\n\n.igv-circview-track-panel {\n z-index: 1024;\n position: absolute;\n top: 33px;\n left: 0;\n width: 100%;\n height: fit-content;\n border-bottom-style: solid;\n border-bottom-color: dimgray;\n border-bottom-width: thin;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n}\n.igv-circview-track-panel > div {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-circview-track-panel > div > div {\n margin: 4px;\n}\n\n.igv-circview-swatch-button {\n cursor: pointer;\n padding: 5px;\n width: 8px;\n height: 8px;\n border: 1px solid #8d8b8b;\n border-radius: 16px;\n}\n\n.igv-circview-button {\n cursor: pointer;\n padding: 5px;\n color: #444;\n vertical-align: middle;\n text-align: center;\n font-family: "Open Sans", sans-serif;\n font-size: 12px;\n border: 1px solid #8d8b8b;\n border-radius: 4px;\n background: #efefef;\n box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\n}\n\n.igv-circview-button:hover {\n background: #efefef;\n box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n.igv-circview-button:active {\n color: #007bff;\n box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n/*# sourceMappingURL=circular-view.css.map */\n',document.head.insertBefore(t,document.head.childNodes[document.head.childNodes.length-1])}()}const vd=t=>t.startsWith("chr")?t.substring(3):t;function wd(t){const e=[],i=[];for(let n of t.wgChromosomeNames){const r=t.getChromosome(n);i.push(Zd(r.name)),e.push({name:r.name,bpLength:r.bpLength})}return e}function _d(t,e,i,n){const r=e.color||"rgb(0,0,255)",s=xo.addAlpha("all"===i.chr?r:Zd(i.chr),n),o=xo.addAlpha(r,n),a=e.name.replaceAll(" ","%20"),l="all"===i.chr?a:`${a} ${i.chr}:${i.start}-${i.end}`;e.browser.circularView.addChords(t,{track:l,color:s,trackColor:o}),e.browser.circularViewVisible||(e.browser.circularViewVisible=!0)}class xd{constructor(t,{minTLENPercentile:e,maxTLENPercentile:i}){this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===e?.1:e,this.up=void 0===i?99.5:i,this.isizes=[],this.compute(t)}compute(t){for(let n of t)if(n.isProperPair()){var e=Math.abs(n.fragmentLength);this.sumF+=e,this.sumF2+=e*e,this.isizes.push(e);var i=n.pairOrientation;if("string"==typeof i&&4===i.length)switch(""+i.charAt(0)+i.charAt(2)){case"FF":case"RR":this.ffCount++;break;case"FR":this.frCount++;break;case"RF":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation="ff":this.frCount/this.totalCount>.9?this.orienation="fr":this.rfCount/this.totalCount>.9&&(this.orienation="rf"),this.minTLEN=0===this.lp?0:kd(this.isizes,this.lp),this.maxTLEN=kd(this.isizes,this.up)}}function kd(t,e){if(0!==t.length){var i=Math.floor(t.length*(e/100));return t.sort((function(t,e){return t-e})),t[i]}}const Sd={getTissueInfo:function(t,e){let i=(e=e||"https://gtexportal.org/rest/v1")+"/dataset/tissueInfo?datasetId="+(t=t||"gtex_v8");return zo.loadJson(i,{})},trackConfiguration:function(t,e){return{type:"eqtl",sourceType:"gtex-ws",url:(e=e||"https://gtexportal.org/rest/v1")+"/association/singleTissueEqtlByLocation",tissueSiteDetailId:t.tissueSiteDetailId,name:t.tissueSiteDetailId.split("_").join(" "),visibilityWindow:25e4}}};function Cd(t,e,i){let n=(t.start-e)/i,r=(t.end-e)/i,s=r-n;return s<3&&(s=3,n-=1.5),{px:n,px1:r,pw:s}}function Ad(t,e,i,n,r,s){try{r.save(),r.fillStyle=this.color,r.strokeStyle=this.color;const n=this.getColorForFeature(t);let o,a;r.fillStyle=n,r.strokeStyle=n,"SQUISHED"===this.displayMode&&void 0!==t.row?(o=this.featureHeight/2,a=this.margin+this.squishedRowHeight*t.row):"EXPANDED"===this.displayMode&&void 0!==t.row?(o=this.featureHeight,a=this.margin+this.expandedRowHeight*t.row):(o=this.featureHeight,a=this.margin);const l=s.pixelWidth,h=a+o/2,c=o/2,u=h-c/2,d=t.exons?t.exons.length:0,f=Cd(t,e,i),p=this.arrowSpacing,g="+"===t.strand?1:"-"===t.strand?-1:0;if(0===d){const t=Math.max(0,f.px),e=Math.min(l,f.px1),i=e-t;if(r.fillRect(t,a,i,o),0!==g){r.fillStyle="white",r.strokeStyle="white";for(let i=t+p/2;il)break;if(d.utr)r.fillRect(m,u,y,c);else if(d.cdStart&&(f=Math.round((d.cdStart-e)/i),r.fillRect(m,u,f-m,c),y-=f-m,m=f),d.cdEnd&&(f=Math.round((d.cdEnd-e)/i),r.fillRect(f,u,b-f,c),y-=b-f,b=f),y=Math.max(y,1),r.fillRect(m,a,y,o),y>p+5&&0!==g){r.fillStyle="white",r.strokeStyle="white";for(let t=m+p/2;tv||p)&&(o.rowLastLabelX[e.row]=y,"y"===o.axis?(t.save(),na.labelTransformWithContext(t,c),na.fillText(t,a,c,u,g,h),t.restore()):na.fillText(t,a,c,u,g,h))}finally{t.restore()}}const Id=new Set(["nonsense","missense","stop-loss","frameshift","cds-indel"]),Ed=new Set(["coding-synon"]),Md=new Set(["splice-3","splice-5"]),Rd=new Set(["untranslated-5","untranslated-3"]);function Ld(t,e,i,n,r){var s,o,a,l,h=Cd(t,e,i),c=this.margin,u=this.snpColors.length;switch(s="squished"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case"function":l=t.func.split(",").map((function(t){return Id.has(t)||Md.has(t)?u-1:Ed.has(t)?u-2:Rd.has(t)?u-3:0})),o=l.reduce((function(t,e){return Math.max(t,e)}));break;case"class":o="deletion"===(a=t.class)?u-1:"mnp"===a?u-2:"microsatellite"===a||"named"===a?u-3:0}r.fillStyle=this.snpColors[o],r.fillRect(h.px,c,h.pw,s)}function Bd(t,e,i,n,r){const s="EXPANDED"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let o=this.margin;"COLLAPSED"!==this.displayMode&&void 0!==t.row&&(o+=t.row*s);const a=o+.5*s,l=a-.5*s,h=a+.5*s,c=Math.round((t.junction_left-e)/i),u=Math.round((t.junction_right-e)/i);r.beginPath(),r.moveTo(c,a),r.bezierCurveTo(c,l,u,l,u,a),r.lineWidth=1+Math.log(t.num_junction_reads)/Math.log(2),r.strokeStyle="blue",r.stroke();const d=t.spanning_frag_coords;for(let t=0;te&&(e=i.row);return this.margin+(e+1)*("SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(t){const e=t.features,i=t.context,n=t.bpPerPixel,r=t.bpStart,s=t.pixelWidth,o=t.pixelHeight,a=r+s*n+1;if(this.config.isMergedTrack||na.fillRect(i,0,t.pixelTop,s,o,{fillStyle:"rgb(255, 255, 255)"}),e){const l=[];t.rowLastX=[],t.rowLastLabelX=[];for(let i of e)if(i.start>r&&i.enda)break;const e="COLLAPSED"===this.displayMode?0:s.row;t.drawLabel=t.labelAllFeatures||h>10;const l=Math.ceil((s.end-r)/n),u=c[e];if(!u||l>u){this.render.call(this,s,r,n,o,i,t);const a=Math.floor((s.start-r)/n);u&&a-u<=0&&(i.globalAlpha=.5,na.strokeLine(i,a,0,a,o,{strokeStyle:"rgb(255, 255, 255)"}),i.globalAlpha=1),c[e]=l}}}else console.log("No feature list")}clickedFeatures(t){const e=t.y-this.margin,i=super.clickedFeatures(t);let n;switch(this.displayMode){case"SQUISHED":n=Math.floor(e/this.squishedRowHeight);break;case"EXPANDED":n=Math.floor(e/this.expandedRowHeight);break;default:n=void 0}return i.filter((function(t){return void 0===n||void 0===t.row||n===t.row}))}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=t.genomicLocation,n=[];for(let t of e){const e=t._f||t,r="function"==typeof e.popupData?e.popupData(i):this.extractPopupData(e);if(r){n.length>0&&n.push("

");const s=this.infoURL||this.config.infoURL;for(let e of r)if(n.push(e),s&&e.name&&"name"===e.name.toLowerCase()&&e.value&&ji(e.value)&&!e.value.startsWith("<")){const i=s.replace("$$",t.name);e.value=`${e.value}`}const o="gff"===this.config.format||"gff3"===this.config.format||"gtf"===this.config.format;if(e.exons)for(let t=0;t=r.start&&i<=r.end){const i=o?r.number:"-"===e.strand?e.exons.length-t:t+1;i&&(n.push("
"),n.push({name:"Exon Number",value:i}));break}}}}return n}menuItemList(){const t=[];if(this.render===Ld){t.push("
");for(let e of["function","class"])t.push({object:fe(zi("Color by "+e,e===this.colorBy)),click:()=>{this.colorBy=e,this.trackView.repaintViews()}})}t.push("
");for(let e of["COLLAPSED","SQUISHED","EXPANDED"]){const i={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};t.push({object:fe(zi(i[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.config.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return t}contextMenuItemList(t){const e=this.clickedFeatures(t);if(void 0===e||0===e.length)return;e.length>1&&e.sort(((t,e)=>e.end-e.start-(t.end-t.start)));const i=e[0];if(i.end-i.start<=1e6){const t=[{label:"View feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(i.chr,i.start,i.end);t?"-"===i.strand&&(t=Ra(t)):t="Unknown sequence",this.browser.alert.present(t)}}];return ba()&&void 0!==navigator.clipboard&&t.push({label:"Copy feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(i.chr,i.start,i.end);t?"-"===i.strand&&(t=Ra(t)):t="Unknown sequence";try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),t.push("
"),t}}description(){if(Ld===this.render){let t=""+this.name+"
";return t+="Color By Function:
",t+='Red: Coding-Non-Synonymous, Splice Site
',t+='Green: Coding-Synonymous
',t+='Blue: Untranslated
',t+='Black: Intron, Locus, Unknown

',t+="Color By Class:
",t+='Red: Deletion
',t+='Green: MNP
',t+='Blue: Microsatellite, Named
',t+='Black: Indel, Insertion, SNP',t+="",t}return super.description()}getColorForFeature(t){let e;if(this.altColor&&"-"===t.strand)e="function"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)e="function"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const i=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];e=this.colorTable.getColor(i)}else t.color&&(e=t.color);if(e||(e="rgb(0, 0, 150)"),t.alpha&&1!==t.alpha)e=xo.addAlpha(e,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const i=function(t,e,i){const n=(e-t)/9,r=Math.floor((i-t)/n);return Math.min(1,.2+.8*r/9)}(this.config.min?this.config.min:this.viewLimitMin?this.viewLimitMin:0,this.config.max?this.config.max:this.viewLimitMax?this.viewLimitMax:1e3,t.score);t.alpha=i,e=xo.addAlpha(e,i)}return e}dispose(){this.trackView=void 0}}class Fd{constructor(t){this.config=t,this.browser=t.browser,this.columnFormat=t.columnFormat,this.tableRowSelectionList=[],this.tableDOM=_e.div({class:"igv-roi-table"}),t.parent.appendChild(this.tableDOM),this.headerDOM=t,this.tableColumnTitles=this.tableDOM,this.tableRowContainer=this.tableDOM,this.footerDOM=t.gotoButtonHandler}set headerDOM({browser:t,parent:e,headerTitle:i,dismissHandler:n}){const r=_e.div();this.tableDOM.appendChild(r);const s=_e.div();r.appendChild(s),s.innerHTML=i;const o=_e.div();r.appendChild(o),o.appendChild(_i.createIcon("times")),this.boundDismissHandler=function(t){t.stopPropagation(),n()}.bind(this),o.addEventListener("click",this.boundDismissHandler);const{y:a}=t.root.getBoundingClientRect(),{y:l}=e.getBoundingClientRect(),h=-(l-a);Ci(this.tableDOM,r,{minX:0,minY:h}),this.tableDOM.style.display="none",this._headerDOM=r}set tableColumnTitles(t){const e=_e.div({class:"igv-roi-table-column-titles"});t.appendChild(e);for(const{label:t,width:i}of this.columnFormat){const n=_e.div();e.appendChild(n),n.style.width=i,n.innerText=t}this._tableColumnTitlesDOM=e}get tableColumnTitles(){return this._tableColumnTitlesDOM}set tableRowContainer(t){const e=_e.div({class:"igv-roi-table-row-container"});t.appendChild(e),this._tableRowContainerDOM=e}get tableRowContainer(){return this._tableRowContainerDOM}set footerDOM(t){const e=_e.div();this.tableDOM.appendChild(e);const i=_e.div({class:"igv-roi-table-button"});e.appendChild(i),i.id="igv-roi-table-view-button",i.textContent="Go To",i.style.pointerEvents="none",this._footerDOM=e,this.gotoButton=i,this.boundGotoButtonHandler=t.bind(this),this.gotoButton.addEventListener("click",this.boundGotoButtonHandler)}tableRowDOMHelper(t){t.addEventListener("mousedown",(e=>{e.stopPropagation(),t.classList.toggle("igv-roi-table-row-selected"),t.classList.contains("igv-roi-table-row-selected")?t.classList.remove("igv-roi-table-row-hover"):t.classList.add("igv-roi-table-row-hover"),this.setTableRowSelectionState(t.classList.contains("igv-roi-table-row-selected"))})),t.addEventListener("mouseover",(e=>{t.classList.contains("igv-roi-table-row-selected")?t.classList.remove("igv-roi-table-row-hover"):t.classList.add("igv-roi-table-row-hover")})),t.addEventListener("mouseout",(e=>{t.classList.remove("igv-roi-table-row-hover")}))}clearTable(){const t=this.tableRowContainer.querySelectorAll(".igv-roi-table-row");for(let e of t)e.remove()}setTableRowSelectionState(t){t?this.tableRowSelectionList.push(1):this.tableRowSelectionList.pop(),this.gotoButton.style.pointerEvents=this.tableRowSelectionList.length>0?"auto":"none"}present(){this.tableDOM.style.left="0px";const{y:t}=this.browser.root.getBoundingClientRect(),{y:e}=this.config.parent.getBoundingClientRect();this.tableDOM.style.top=t-e+"px",this.tableDOM.style.display="flex"}dismiss(){this.tableDOM.style.display="none"}dispose(){this.tableDOM.innerHTML="",this.tableDOM.remove();for(const t of Object.keys(this))this[t]=void 0;document.removeEventListener("click",this.boundDismissHandler)}}class Od extends Fd{constructor(t){super(Object.assign({width:"1024px"},t)),this.descriptionDOM=t}set descriptionDOM(t){if(t.description){let e;e=_e.div({class:"igv-roi-table-description"}),this.tableDOM.insertBefore(e,this.tableColumnTitles),e.style.height="auto",e.innerHTML="BLAT result for query sequence:",e=_e.div({class:"igv-roi-table-description"}),this.tableDOM.insertBefore(e,this.tableColumnTitles),e.style.height="auto",e.style.maxHeight="128px",e.innerHTML=t.description,e=_e.div({class:"igv-roi-table-goto-explainer"}),this.tableDOM.insertBefore(e,this.tableColumnTitles),e.innerHTML="Select one or more rows and click Go To to view the regions"}}tableRowDOM(t){const e=_e.div({class:"igv-roi-table-row"}),i=t.map((t=>isFinite(t)?$i(t):t));for(let t=0;tt.remove())),t.length>0)for(let e of t){const t=this.tableRowDOM(e);this.tableRowContainer.appendChild(t)}}static getColumnFormatConfiguration(){return[{label:"chr",width:"7%"},{label:"start",width:"12%"},{label:"end",width:"12%"},{label:"strand",width:"5%"},{label:"score",width:"5%"},{label:"match",width:"5%"},{label:"mis-match",width:"7%"},{label:"rep. match",width:"7%"},{label:"N's",width:"3%"},{label:"Q gap count",width:"9%"},{label:"Q gap bases",width:"9%"},{label:"T gap count",width:"9%"},{label:"T gap bases",width:"9%"}]}static gotoButtonHandler(t){t.stopPropagation();const e=this.tableDOM.querySelectorAll(".igv-roi-table-row-selected"),i=[];for(const t of e){const e=[];t.querySelectorAll("div").forEach((t=>e.push(t.innerText)));const[n,r,s]=e;i.push(`${n}:${r}-${s}`)}for(const t of this.tableDOM.querySelectorAll(".igv-roi-table-row"))t.classList.remove("igv-roi-table-row-selected");this.setTableRowSelectionState(!1),this.browser.search(i.join(" "))}}const Dd="https://igv.org/services/blatUCSC.php";async function Pd({url:t,userSeq:e,db:i}){t=t||Dd;const n=await async function(t="",e,i){const n=new URLSearchParams;n.append("userSeq",e),n.append("db",i);return(await fetch(t,{method:"post",body:n})).json()}(t,e,i);return n.fields,n.blat.map(Wl)}const zd=25e3;class Ud extends Nd{constructor(t,e){super(t,e),this.name||(this.name="Blat Results"),this.sequence=t.sequence,this.table=void 0}openTableView(){if(void 0===this.table){const t=this.config.features.map((t=>[t.chr,t.start+1,t.end,t.strand,t.score,t.matches,t.misMatches,t.repMatches,t.nCount,t.qNumInsert,t.qBaseInsert,t.tNumInsert,t.tBaseInsert])),e={browser:this.browser,parent:this.browser.parent,headerTitle:this.config.title,description:this.sequence,dismissHandler:()=>{this.table.dismiss(),this.table.dispose(),this.table=void 0},columnFormat:Od.getColumnFormatConfiguration(),gotoButtonHandler:Od.gotoButtonHandler};this.table=new Od(e),this.table.renderTable(t)}this.table.present()}menuItemList(){const t=super.menuItemList();return t.push("
"),t.push({label:"Open table view",click:()=>this.openTableView()}),t}dispose(){super.dispose(),this.table&&this.table.popover.parentElement.removeChild(this.table.popover)}}async function Vd({sequence:t,browser:e,name:i,title:n}){if(t.length>zd)return void e.alert.present(`Sequence size exceeds maximum allowed length (${t.length} > 25000)`);const r=e.genome.id,s=e.config.blatServerURL;try{const o={type:"blat",name:i||"blat results",title:n||"blat results",sequence:t,altColor:"rgb(176, 176, 236)",color:"rgb(236, 176, 176)",features:await Pd({url:s,userSeq:t,db:r})};(await e.loadTrack(o)).openTableView()}catch(t){e.alert.present(`Error performing blat search: ${t}`)}}const Hd="rgb(185, 185, 185)";class jd extends ch{static defaults={alleleFreqThreshold:.2,visibilityWindow:3e4,showCoverage:!0,showAlignments:!0,viewAsPairs:!1,pairsSupported:!0,showSoftClips:!1,showAllBases:!1,showInsertions:!0,showMismatches:!0,height:300,coverageTrackHeight:50};constructor(t,e){super(t,e)}init(t){this.type="alignment",this.featureSource=new ju(t,this.browser),this.coverageTrack=new $d(t,this),this.alignmentTrack=new qd(t,this),super.init(t),this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.showAlignments||(this._height=this.coverageTrackHeight),t.sort&&(Array.isArray(t.sort)?this.assignSort(t.sort[0]):this.assignSort(t.sort))}set height(t){this._height=t,this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?t-this.coverageTrackHeight:t)}get height(){return this._height}get minTemplateLength(){const t=void 0!==this.config.minTLEN?this.config.minTLEN:this.config.minFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.minTLEN:0}get maxTemplateLength(){const t=void 0!==this.config.maxTLEN?this.config.maxTLEN:this.config.maxFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.maxTLEN:1e3}sort(t){t=this.assignSort(t);for(let e of this.trackView.viewports)if(e.containsPosition(t.chr,t.position)){const i=e.cachedFeatures;i&&(i.sortRows(t),e.repaint())}}assignSort(t){if(t.locus){const e=function(t){const e=t.split(":"),i=e[1].split("-"),n={chr:e[0],start:Number.parseInt(i[0].replace(/,/g,""))-1};return i.length>1?n.end=Number.parseInt(i[1].replace(/,/g,"")):n.end=n.start+1,n}(t.locus);t.chr=e.chr,t.position=e.start}else t.position--;return t.direction="ASC"===t.direction||!0===t.direction,t.chr=this.browser.genome.getChromosomeName(t.chr),this.sortObject=t,this.sortObject}async getFeatures(t,e,i,n,r){const s=await this.featureSource.getAlignments(t,e,i);if(s.paired&&!this._pairedEndStats&&!this.config.maxFragmentLength){const t=new xd(s.alignments,this.config);t.totalCount>99&&(this._pairedEndStats=t)}s.alignments=void 0;const o=this.sortObject;return o&&o.chr===t&&o.position>=e&&o.position<=i&&s.sortRows(o),s}computePixelHeight(t){return(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(t):0)}draw(t){na.fillRect(t.context,0,t.pixelTop,t.pixelWidth,t.pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),!0===this.showCoverage&&this.coverageTrackHeight>0?(this.trackView.axisCanvas.style.display="block",this.coverageTrack.draw(t)):this.trackView.axisCanvas.style.display="none",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(t))}paintAxis(t,e,i){this.coverageTrack.paintAxis(t,e,this.coverageTrackHeight)}contextMenuItemList(t){return this.alignmentTrack.contextMenuItemList(t)}popupData(t){return!0===this.showCoverage&&t.y>=this.coverageTrack.top&&t.y=this.coverageTrack.top&&t.y=this.coverageTrack.top&&t.y");const e=fe('
');e.text("Color by:"),t.push({name:void 0,object:e,click:void 0,init:void 0});const i=[{key:"strand",label:"read strand"}];this.alignmentTrack.hasPairs&&(i.push({key:"firstOfPairStrand",label:"first-of-pair strand"}),i.push({key:"pairOrientation",label:"pair orientation"}),i.push({key:"tlen",label:"insert size (TLEN)"}),i.push({key:"unexpectedPair",label:"pair orientation & insert size (TLEN)"}));const n="tag"+(this.alignmentTrack.colorByTag?" ("+this.alignmentTrack.colorByTag+")":"");i.push({key:"tag",label:n});for(let e of i){const i=this.alignmentTrack.colorBy===e.key;t.push(this.colorByCB(e,i))}const r=()=>{if(!this.autoHeight){const t=(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(t)}};t.push("
"),t.push({object:fe(zi("Show Coverage",this.showCoverage)),click:()=>{this.showCoverage=!this.showCoverage,r(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:fe(zi("Show Alignments",this.showAlignments)),click:()=>{this.showAlignments=!this.showAlignments,r(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push("
"),t.push({object:fe(zi("Show all bases",this.showAllBases)),click:()=>{this.showAllBases=!this.showAllBases,this.config.showAllBases=this.showAllBases,this.trackView.repaintViews()}}),t.push("
"),t.push({object:fe(zi("Show mismatches",this.showMismatches)),click:()=>{this.showMismatches=!this.showMismatches,this.config.showMismatches=this.showMismatches,this.trackView.repaintViews()}}),t.push({object:fe(zi("Show insertions",this.showInsertions)),click:()=>{this.showInsertions=!this.showInsertions,this.config.showInsertions=this.showInsertions,this.getCachedAlignmentContainers(),this.trackView.repaintViews()}}),t.push({object:fe(zi("Show soft clips",this.showSoftClips)),click:()=>{this.showSoftClips=!this.showSoftClips,this.config.showSoftClips=this.showSoftClips,this.featureSource.setShowSoftClips(this.showSoftClips);const t=this.getCachedAlignmentContainers();for(let e of t)e.setShowSoftClips(this.showSoftClips);this.trackView.repaintViews()}}),this.pairsSupported&&this.alignmentTrack.hasPairs&&(t.push("
"),t.push({object:fe(zi("View as pairs",this.viewAsPairs)),click:()=>{this.viewAsPairs=!this.viewAsPairs,this.config.viewAsPairs=this.viewAsPairs,this.featureSource.setViewAsPairs(this.viewAsPairs);const t=this.getCachedAlignmentContainers();for(let e of t)e.setViewAsPairs(this.viewAsPairs);this.trackView.repaintViews()}})),this.browser.circularView&&(this.alignmentTrack.hasPairs||this.alignmentTrack.hasSupplemental)&&(t.push("
"),this.alignmentTrack.hasPairs&&t.push({label:"Add discordant pairs to circular view",click:()=>{for(let t of this.trackView.viewports)this.addPairedChordsForViewport(t)}}),this.alignmentTrack.hasSupplemental&&t.push({label:"Add split reads to circular view",click:()=>{for(let t of this.trackView.viewports)this.addSplitChordsForViewport(t)}})),t.push("
");const s=fe('
');return s.text("Display mode:"),t.push({name:void 0,object:s,click:void 0,init:void 0}),t.push({object:fe(zi("expand","EXPANDED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="EXPANDED",this.config.displayMode="EXPANDED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:fe(zi("squish","SQUISHED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="SQUISHED",this.config.displayMode="SQUISHED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t}colorByCB(t,e){return{name:void 0,object:fe(zi(t.label,e)),click:e=>{"tag"!==t.key?t.key===this.alignmentTrack.colorBy?(this.alignmentTrack.colorBy="none",this.config.colorBy="none",this.trackView.repaintViews()):(this.alignmentTrack.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews()):this.browser.inputDialog.present({label:"Tag Name",value:this.alignmentTrack.colorByTag?this.alignmentTrack.colorByTag:"",callback:t=>{t?(this.alignmentTrack.colorBy="tag",this.alignmentTrack.colorByTag=t,this.alignmentTrack.tagColors||(this.alignmentTrack.tagColors=new ta("Set1"))):(this.alignmentTrack.colorBy="none",this.alignmentTrack.colorByTag=""),this.trackView.repaintViews()}},e)},init:void 0}}getState(){const t=super.getState();return this.sortObject&&(t.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?"ASC":"DESC"}),t}getCachedAlignmentContainers(){return this.trackView.viewports.map((t=>t.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(t){this.coverageTrack.dataRange=t}get logScale(){return this.coverageTrack.logScale}set logScale(t){this.coverageTrack.logScale=t}get autoscale(){return this.coverageTrack.autoscale}set autoscale(t){this.coverageTrack.autoscale=t}addPairedChordsForViewport(t){const e=this.maxTemplateLength,i=[],n=t.referenceFrame;for(let r of t.cachedFeatures.allAlignments())r.end>=n.start&&r.start<=n.end&&(r.paired?r.end-r.start>e&&i.push(r):r.mate&&r.mate.chr&&(r.mate.chr!==r.chr||Math.max(r.fragmentLength)>e)&&i.push(r));_d((t=>{const e=[];for(let i of t)if(i.paired)i.firstAlignment&&i.secondAlignment&&e.push({uniqueId:i.readName,refName:vd(i.firstAlignment.chr),start:i.firstAlignment.start,end:i.firstAlignment.end,mate:{refName:vd(i.secondAlignment.chr),start:i.secondAlignment.start,end:i.secondAlignment.end}});else{const t=i.mate;t&&t.chr&&t.position&&e.push({uniqueId:i.readName,refName:vd(i.chr),start:i.start,end:i.end,mate:{refName:vd(t.chr),start:t.position-1,end:t.position}})}return e})(i),this,n,.02)}addSplitChordsForViewport(t){const e=[],i=t.referenceFrame;for(let n of t.cachedFeatures.allAlignments()){const t=n.hasTag("SA");n.end>=i.start&&n.start<=i.end&&t&&e.push(n)}_d((t=>{const e=t=>{const e=hu(t.tags().SA);let n=0;for(let r of e)r.start!==t.start&&i.push({uniqueId:`${t.readName}_${n++}`,refName:vd(t.chr),start:t.start,end:t.end,mate:{refName:vd(r.chr),start:r.start,end:r.start+r.lenOnRef}})},i=[];for(let i of t)i.paired?(e(i.firstAlignment),i.secondAlignment&&e(i.secondAlignment)):e(i);return i})(e),this,i,.02)}}class $d{constructor(t,e){this.parent=e,this.featureSource=e.featureSource,this.paintAxis=$u,this.top=0,this.autoscale=t.autoscale||void 0===t.max,this.autoscale||(this.dataRange={min:t.min||0,max:t.max})}get height(){return this.parent.coverageTrackHeight}draw(t){const e=t.pixelTop;t.pixelHeight;const i=this.parent.browser.nucleotideColors;if(e>this.height)return;const n=t.context,r=t.features.coverageMap;let s;r.refSeq&&(s=r.refSeq.toUpperCase());const o=t.bpPerPixel,a=t.bpStart,l=a+t.pixelWidth*o+1;let h;h=this.parent.coverageColor?this.parent.coverageColor:this.parent.color&&"function"!=typeof this.parent.color?xo.darkenLighten(this.parent.color,-35):"rgb(150, 150, 150)",na.setProperties(n,{fillStyle:h,strokeStyle:h});const c=Math.max(1,Math.ceil(1/o));for(let t=0,e=r.coverage.length;tl)break;const i=r.coverage[t];if(!i)continue;const s=Math.round(i.total/this.dataRange.max*this.height),h=this.height-s,u=Math.floor((e-a)/o);na.fillRect(n,u,h,c,s)}if(s)for(let t=0,e=r.coverage.length;tl)break;const h=r.coverage[t];if(!h)continue;const u=h.total/this.dataRange.max*this.height;let d=this.height-u;const f=Math.floor((e-a)/o),p=s[t];if(h.isMismatch(p)){na.setProperties(n,{fillStyle:i[p]}),na.fillRect(n,f,d,c,u);let t=0;for(let e of["A","C","T","G"]){const r=(h["pos"+e]+h["neg"+e])/this.dataRange.max*this.height;d=this.height-r-t,t+=r,na.setProperties(n,{fillStyle:i[e]}),na.fillRect(n,f,d,c,r)}}}}getClickedObject(t){let e=t.viewport.cachedFeatures;if(!e||0===e.length)return;const i=Math.floor(t.genomicLocation),n=e.coverageMap,r=Math.floor(i-n.bpStart);return n.coverage[r]}popupData(t){const e=[],i=this.getClickedObject(t);if(i){const n=Math.floor(t.genomicLocation),r=t.viewport.referenceFrame;e.push(r.chr+":"+$i(1+n)),e.push({name:"Total Count",value:i.total});let s=i.posA+i.negA;s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posA+"+, "+i.negA+"- )"),e.push({name:"A",value:s}),s=i.posC+i.negC,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posC+"+, "+i.negC+"- )"),e.push({name:"C",value:s}),s=i.posG+i.negG,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posG+"+, "+i.negG+"- )"),e.push({name:"G",value:s}),s=i.posT+i.negT,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posT+"+, "+i.negT+"- )"),e.push({name:"T",value:s}),s=i.posN+i.negN,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posN+"+, "+i.negN+"- )"),e.push({name:"N",value:s}),e.push("
"),e.push({name:"DEL",value:i.del.toString()}),e.push({name:"INS",value:i.ins.toString()})}return e}}class qd{constructor(t,e){this.parent=e,this.browser=e.browser,this.featureSource=e.featureSource,this.top=0===t.coverageTrackHeight?0:t.coverageTrackHeight+5,this.displayMode=t.displayMode||"EXPANDED",this.alignmentRowHeight=t.alignmentRowHeight||14,this.squishedRowHeight=t.squishedRowHeight||3,this.negStrandColor=t.negStrandColor||"rgba(150, 150, 230, 0.75)",this.posStrandColor=t.posStrandColor||"rgba(230, 150, 150, 0.75)",this.insertionColor=t.insertionColor||"rgb(138, 94, 161)",this.insertionTextColor=t.insertionTextColor||"white",this.showInsertionText=void 0!==t.showInsertionText&&!!t.showInsertionText,this.deletionColor=t.deletionColor||"black",this.deletionTextColor=t.deletionTextColor||"black",this.showDeletionText=void 0!==t.showDeletionText&&!!t.showDeletionText,this.skippedColor=t.skippedColor||"rgb(150, 170, 170)",this.pairConnectorColor=t.pairConnectorColor,this.smallTLENColor=t.smallTLENColor||t.smallFragmentLengthColor||"rgb(0, 0, 150)",this.largeTLENColor=t.largeTLENColor||t.largeFragmentLengthColor||"rgb(200, 0, 0)",this.pairOrientation=t.pairOrienation||"fr",this.pairColors={},this.pairColors.RL=t.rlColor||"rgb(0, 150, 0)",this.pairColors.RR=t.rrColor||"rgb(20, 50, 200)",this.pairColors.LL=t.llColor||"rgb(0, 150, 150)",this.colorBy=t.colorBy||"unexpectedPair",this.colorByTag=t.colorByTag?t.colorByTag.toUpperCase():void 0,this.bamColorTag=void 0===t.bamColorTag?"YC":t.bamColorTag,this.hideSmallIndels=t.hideSmallIndels,this.indelSizeThreshold=t.indelSizeThreshold||1,this.hasPairs=!1,this.hasSupplemental=!1}setTop(t,e){this.top=0===t.height||!1===e?0:5+t.height}computePixelHeight(t){return t.packedAlignmentRows?(t.hasDownsampledIntervals()?10:0)+("SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight)*t.packedAlignmentRows.length+5:0}draw(t){const e=t.features,i=t.context,n=t.bpPerPixel,r=t.bpStart,s=t.pixelWidth,o=r+s*n+1,a=this.parent.showSoftClips,l=this.parent.showAllBases,h=this.browser.nucleotideColors,c=e.packedAlignmentRows;i.save();let u=e.sequence;u&&(u=u.toUpperCase());let d=0,f=t.pixelTop;this.top&&i.translate(0,this.top);const p=f+t.pixelHeight;e.hasDownsampledIntervals()?(d=10,e.downsampledIntervals.forEach((function(t){var e=(t.start-r)/n,s=(t.end-r)/n;s-e>5&&(e+=1,s-=1),na.fillRect(i,e,2,s-e,3,{fillStyle:"black"})}))):d=0,this.alignmentsYOffset=d;const g="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;if(c){const t=c.length;for(let e=0;ep)break;if(!(i+no)break;!0!==e.hidden&&(e instanceof Xc?(m.call(this,e,i,n),b.call(this,e.firstAlignment,i,n),e.secondAlignment&&b.call(this,e.secondAlignment,i,n)):b.call(this,e,i,n))}}}function m(t,e,s){var a=this.getConnectorColor(t.firstAlignment),l=(t.connectingStart-r)/n,h=(t.connectingEnd-r)/n,c=e+s/2;t.connectingEndo||(t.mq<=0&&(a=xo.addAlpha(a,.15)),na.setProperties(i,{fillStyle:a,strokeStyle:a}),na.strokeLine(i,l,c,h,c))}function b(t,c,d){if(t.start+t.lengthOnRefo)return;const f=a?t.blocks:t.blocks.filter((t=>"S"!==t.type));let p=this.getAlignmentColor(t);const m=p;t.mq<=0&&(p=xo.addAlpha(p,.15)),na.setProperties(i,{fillStyle:p,strokeStyle:m});const b=[];for(let t=0;to))break}if(t.gaps){const e=c+d/2;for(let s of t.gaps){const t=(s.start-r)/n,o=(s.start+s.len-r)/n,a=o-t,l=s.len.toString(),h=6*l.length,u=t+a/2,d="D"===s.type?this.deletionColor:this.skippedColor;if(na.strokeLine(i,t,e,o,e,{strokeStyle:d,lineWidth:2}),this.showDeletionText&&s.len>1&&a>=h+8){const t=u-h/2;na.fillRect(i,t-1,c-1,h+2,12,{fillStyle:"white"}),na.fillText(i,l,t,c+10,{font:"normal 10px monospace",fillStyle:this.deletionTextColor})}}}if(t.insertions&&this.parent.showInsertions){let e=-1;for(let s of t.insertions){if(this.hideSmallIndels&&s.len<=this.indelSizeThreshold)continue;if(s.starto)break;const t=s.start-r,a=s.len.toString(),l=2+6*a.length,h=this.showInsertionText&&1!==s.len?Math.round(s.len/n):2,u=Math.max(Math.min(l,h),2),f=t/n-u/2;if(f-e>2){const t={fillStyle:this.insertionColor};na.fillRect(i,f-2,c,u+4,2,t),na.fillRect(i,f,c+2,u,d-4,t),na.fillRect(i,f-2,c+d-2,u+4,2,t),this.showInsertionText&&s.len>1&&h>l&&na.fillText(i,a,f+1,c+10,{font:"normal 10px monospace",fillStyle:this.insertionTextColor}),e=f}}}function y(o,a){const b=[],y=o.start-e.start,v=(o.start-r)/n,w=(o.start+o.len-r)/n,_=Math.max(1,w-v),x=100/n,k=Math.min(g/2,x/6),S="S"===o.type,C=t.mq<=0||this.highlightedAlignmentReadNamed===t.readName||S;let A=m;this.highlightedAlignmentReadNamed===t.readName?A="red":S&&(A="rgb(50,50,50)");const T=!0===t.strand&&a===f.length-1,I=!1===t.strand&&0===a;if(T|I){let t,e;T?(t=[v,w,w+k,w,v,v],e=[c,c,c+d/2,c+d,c+d,c]):I&&(t=[w,v,v-k,v,w,w],e=[c,c,c+d/2,c+d,c+d,c]),na.fillPolygon(i,t,e,{fillStyle:p}),C&&na.strokePolygon(i,t,e,{strokeStyle:A})}else na.fillRect(i,v,c,_,d,{fillStyle:p}),C&&(i.save(),i.strokeStyle=A,i.strokeRect(v,c,_,d),i.restore());if(S||l||this.parent.showMismatches&&u&&t.seq&&"*"!==t.seq){const e=t.seq?t.seq.toUpperCase():void 0,i=t.qual,a=o.seqOffset,f=Math.max(1,1/n);for(let t=0,p=o.len;ts)break;let g=e?e.charAt(a+t):"";const m=y+t>=0?u.charAt(y+t):"";if("="===g&&(g=m),"X"===g||m!==g||S||l){let e;e=!S&&void 0!==i&&i.length>a+t?Wd(i[a+t],h[g]):h[g],e&&b.push({bbox:{x:p,y:c,width:f,height:d},baseColor:e,readChar:g})}}}return b}b.forEach((({bbox:t,baseColor:e,readChar:r})=>{!function(t,e,i,n,r){var s;if(e<=.1&&i.height>=8){const e=Math.min(10,i.height);t.font=e+"px sans-serif",s=i.x+i.width/2,na.strokeText(t,r,s-t.measureText(r).width/2,e-1+i.y,{strokeStyle:n})}else na.fillRect(t,i.x,i.y,i.width,i.height,{fillStyle:n})}(i,n,t,e,r)}))}i.restore()}popupData(t){const e=this.getClickedObject(t);return e?e.popupData(t.genomicLocation):void 0}contextMenuItemList(t){const e=t.viewport,i=[],n=i=>{const n=this.parent.sortObject,r=!n||n.position!==Math.floor(t.genomicLocation)||!n.direction,s={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:i,direction:r};this.parent.sortObject=s,e.cachedFeatures.sortRows(s),e.repaint()};i.push("Sort by..."),i.push({label:"  base",click:()=>n("BASE")}),i.push({label:"  read strand",click:()=>n("STRAND")}),i.push({label:"  insert size",click:()=>n("INSERT_SIZE")}),i.push({label:"  gap size",click:()=>n("GAP_SIZE")}),i.push({label:"  chromosome of mate",click:()=>n("MATE_CHR")}),i.push({label:"  mapping quality",click:()=>n("MQ")}),i.push({label:"  read name",click:()=>n("READ_NAME")}),i.push({label:"  aligned read length",click:()=>n("ALIGNED_READ_LENGTH")}),i.push({label:"  tag",click:()=>{const i=this.parent.sortObject,n=!i||i.position!==Math.floor(t.genomicLocation)||!i.direction,r={label:"Tag Name",value:this.sortByTag?this.sortByTag:"",callback:i=>{if(i){const r={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:"TAG",tag:i,direction:n};this.sortByTag=i,this.parent.sortObject=r,e.cachedFeatures.sortRows(r),e.repaint()}}};this.browser.inputDialog.present(r,t.event)}}),i.push("
");const r=this.getClickedObject(t);if(r){const e=this.parent.showSoftClips,n="function"==typeof r.alignmentContaining?r.alignmentContaining(t.genomicLocation,e):r;if(n){n.isPaired()&&n.isMateMapped()&&i.push({label:"View mate in split screen",click:()=>{if(n.mate){const e=t.viewport.referenceFrame;if(this.browser.genome.getChromosome(n.mate.chr)){this.highlightedAlignmentReadNamed=n.readName;const t=e.end-e.start,i=n.mate.position-t/2,r=n.mate.position+t/2;this.browser.addMultiLocusPanel(n.mate.chr,i,r,e)}else this.browser.alert.present(`Reference does not contain chromosome: ${n.mate.chr}`)}},init:void 0}),i.push({label:"View read sequence",click:()=>{const t=n.seq;t&&"*"!==t?this.browser.alert.present(t):this.browser.alert.present("Read sequence: *")}}),ba()&&i.push({label:"Copy read sequence",click:async()=>{const t=n.seq;try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}});const e=n.seq;if(e&&"*"!=e){e.length{const t=n.isNegativeStrand()?Ra(e):e,i=`${n.readName} - blat`,r=`${this.parent.name} - ${i}`;Vd({sequence:t,browser:this.browser,name:i,title:r})}});const t=n.softClippedBlocks();t.left&&t.left.len>20&&t.left.len{const i=e.substr(t.left.seqOffset,t.left.len),r=n.isNegativeStrand()?Ra(i):i,s=`${n.readName} - blat left clip`,o=`${this.parent.name} - ${s}`;Vd({sequence:r,browser:this.browser,name:s,title:o})}}),t.right&&t.right.len>20&&t.right.len{const i=e.substr(t.right.seqOffset,t.right.len),r=n.isNegativeStrand()?Ra(i):i,s=`${n.readName} - blat right clip`,o=`${this.parent.name} - ${s}`;Vd({sequence:r,browser:this.browser,name:s,title:o})}})}i.push("
")}}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&i.push({label:"Add discordant pairs to circular view",click:()=>{this.parent.addPairedChordsForViewport(e)}}),this.hasSupplemental&&i.push({label:"Add split reads to circular view",click:()=>{this.parent.addSplitChordsForViewport(e)}}),i.push("
")),i}getClickedObject(t){const e=t.viewport,i=t.y,n=t.genomicLocation,r=this.parent.showSoftClips;let s=e.cachedFeatures;if(!s||0===s.length)return;let o=s.packedAlignmentRows,a=s.downsampledIntervals;const l="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let h=Math.floor((i-this.top-this.alignmentsYOffset)/l);if(h<0){for(let t=0;t=n)return a[t]}else if(ht.containsLocation(n,r)));if(t.length>0)return t[0]}}getConnectorColor(t){if(this.pairConnectorColor)return this.pairConnectorColor;switch(this.colorBy){case"strand":case"firstOfPairStrand":case"pairOrientation":case"tag":return this.parent.color?"function"==typeof this.parent.color?this.parent.color(t):this.parent.color:"rgb(200, 200, 200)";default:return this.getAlignmentColor(t)}}getAlignmentColor(t){let e=Hd;e=this.parent.color?"function"==typeof this.parent.color?this.parent.color(t):this.parent.color:Hd;const i=this.colorBy;switch(i){case"strand":e=t.strand?this.posStrandColor:this.negStrandColor;break;case"firstOfPairStrand":t instanceof Xc?e=t.firstOfPairStrand()?this.posStrandColor:this.negStrandColor:t.isPaired()&&(t.isFirstOfPair()?e=t.strand?this.posStrandColor:this.negStrandColor:t.isSecondOfPair()?e=t.strand?this.negStrandColor:this.posStrandColor:console.error("ERROR. Paired alignments are either first or second."));break;case"unexpectedPair":case"pairOrientation":if(this.pairOrientation&&t.pairOrientation){const i=Gd[this.pairOrientation];if(i){const n=this.pairColors[i[t.pairOrientation]];if(n){e=n;break}}}if("pairOrientation"===i)break;case"tlen":case"fragmentLength":t.mate&&t.isMateMapped()&&(t.mate.chr!==t.chr?e=Zd(t.mate.chr):this.parent.minTemplateLength&&Math.abs(t.fragmentLength)this.parent.maxTemplateLength&&(e=this.largeTLENColor));break;case"tag":const n=t.tags()[this.colorByTag];void 0!==n&&(this.bamColorTag===this.colorByTag?e="rgb("+n+")":(this.tagColors||(this.tagColors=new ta("Set1")),e=this.tagColors.getColor(n)))}return e}}function Wd(t,e){let i;return i=t<5?.1:Math.max(.1,Math.min(1,.1+.9*(t-5)/15)),i=Math.round(10*i)/10,i<1&&(e=xo.addAlpha(e,i)),e}const Gd={fr:{F1R2:"LR",F2R1:"LR",F1F2:"LL",F2F1:"LL",R1R2:"RR",R2R1:"RR",R1F2:"RL",R2F1:"RL"},rf:{R1F2:"LR",R2F1:"LR",R1R2:"LL",R2R1:"LL",F1F2:"RR",F2F1:"RR",F1R2:"RL",F2R1:"RL"},ff:{F2F1:"LR",R1R2:"LR",F2R1:"LL",R1F2:"LL",R2F1:"RR",F1R2:"RR",R2R1:"RL",F1F2:"RL"}};function Zd(t){if(Yd[t])return Yd[t];if(Yd["chr"+t]){const e=Yd["chr"+t];return Yd[t]=e,e}{const e=xo.randomRGB(0,255);return Yd[t]=e,e}}const Yd={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0)",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};let Qd,Xd;class Kd extends ml{constructor(t,e,i,n){super(t,e,i,n)}get contentDiv(){return this.$viewport.get(0)}initializationHelper(){let t;this.$multiLocusCloseButton=fe("
",{class:"igv-multi-locus-close-button"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(_i.createIcon("times-circle")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=fe("
",{class:"igv-multi-locus-ruler-label"}),this.$viewport.append(this.$rulerLabel),t=document.createElement("div"),this.$rulerLabel.append(fe(t)),this.$rulerLabel.get(0).addEventListener("click",(async t=>{t.stopPropagation(),await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=fe("
",{class:"igv-ruler-tooltip"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=fe("
"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new Qc(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(ul.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(t){this.$multiLocusCloseButton.show(),this.$rulerLabel.show(),this.$rulerLabel.get(0).style.backgroundColor=Zd(this.referenceFrame.chr);const e=this.$rulerLabel.get(0).querySelector("div"),{width:i}=this.$rulerLabel.get(0).getBoundingClientRect();e.innerHTML=`${this.referenceFrame.getMultiLocusLabel(t)}`;const{width:n}=e.getBoundingClientRect();n/i>.5&&(e.innerHTML=`${this.referenceFrame.getMultiLocusLabelBPLengthOnly(t)}`)}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(t){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===t){const t=this.browser.referenceFrameList.indexOf(this.referenceFrame),e=`click${this.namespace}`;this.$viewport.on(e,(e=>{const{x:i}=_e.translateMouseCoordinates(e,this.$viewport.get(0)),n=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(i));let r;const{chr:s}=this.browser.genome.getChromosomeCoordinate(n);if(1===this.browser.referenceFrameList.length)r=s;else{let e=this.browser.referenceFrameList.map((({locusSearchString:t})=>t));e[t]=s,r=e.join(" ")}this.browser.search(r)})),this.$viewport.get(0).style.cursor="pointer"}else this.$viewport.get(0).style.cursor="default"}mouseMove(t){if(!0===this.browser.cursorGuideVisible){if(void 0===Xd?(Xd=this,this.$tooltip.show()):Xd.guid!==this.guid?(Xd.$tooltip&&Xd.$tooltip.hide(),this.$tooltip.show(),Xd=this):this.$tooltip.show(),this.browser.isMultiLocusWholeGenomeView()||ul.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:e}=_e.translateMouseCoordinates(t,this.$viewport.get(0)),{start:i,bpPerPixel:n}=this.referenceFrame,r=Math.round(.5+i+Math.max(0,e)*n);this.$tooltipContent.text($i(r));const{width:s}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:o}=this.$viewport.get(0).getBoundingClientRect();this.$tooltip.css({left:`${yo(e,0,o-s)}px`}),clearTimeout(Qd),Qd=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4)}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class Jd extends ml{constructor(t,e,i,n){super(t,e,i,n)}initializationHelper(){this.canvas=document.createElement("canvas"),this.canvas.className="igv-ideogram-canvas",this.$viewport.append(fe(this.canvas)),this.ideogram_ctx=this.canvas.getContext("2d"),this.addMouseHandlers()}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(t){this.boundClickHandler=function(t){const{xNormalized:e,width:i}=_e.translateMouseCoordinates(t,this.ideogram_ctx.canvas),{bpLength:n}=this.browser.genome.getChromosome(this.referenceFrame.chr),r=this.referenceFrame.bpPerPixel*i/n;let s=e;s-r/2<0&&(s=r/2),s+r/2>1&&(s=1-r/2);const o=Math.round((s-r/2)*n),a=Math.round((s+r/2)*n);this.referenceFrame.start=o,this.referenceFrame.end=a,this.referenceFrame.bpPerPixel=(a-o)/i,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),t.addEventListener("click",this.boundClickHandler)}setWidth(t){this.$viewport.width(t)}drawSVGWithContext(t,e,i,n,r,s,o){t.saveWithTranslationAndClipRect(n,r,s,e,i,o),this.trackView.track.draw({context:t,referenceFrame:this.referenceFrame,pixelWidth:e,pixelHeight:i}),t.restore()}repaint(){this.draw({referenceFrame:this.referenceFrame})}draw({referenceFrame:t}){na.configureHighDPICanvas(this.ideogram_ctx,this.$viewport.width(),this.$viewport.height()),this.trackView.track.draw({context:this.ideogram_ctx,referenceFrame:t,pixelWidth:this.$viewport.width(),pixelHeight:this.$viewport.height()})}startSpinner(){}stopSpinner(){}}function tf(t,e,i,n){return"ruler"===t.track.type?new Kd(t,e,i,n):"ideogram"===t.track.id?new Jd(t,e,i,n):new ml(t,e,i,n)}const ef={textAlign:"start",textBaseline:"bottom",strokeStyle:"black",fillStyle:"black"};class nf{constructor(t,e,i,n){this.guid=_e.guid(),this.trackView=t,this.browser=t.browser,this.viewport=_e.div({class:"igv-viewport"}),e.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement("canvas"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext("2d"),this.trackScrollDelta=0,this.contentTop=0,this.setWidth(n),!1===this.browser.showSampleNames&&this.hide(),this.addMouseHandlers()}checkCanvas(){const t=window.devicePixelRatio,e=this.viewport.clientHeight,i=this.browser.sampleNameViewportWidth;if(this.canvas.width!==i*t||this.canvas.height!==e*t){const n=this.canvas;n.width=i*t,n.height=e*t,n.style.width=`${i}px`,n.style.height=`${e}px`,this.ctx=this.canvas.getContext("2d"),this.ctx.scale(t,t)}}setTop(t){if("function"==typeof this.trackView.track.getSamples){this.contentTop=t;const e=this.trackView.track.getSamples();this.repaint(e)}}setWidth(t){this.viewport.innerWidth=t,this.checkCanvas()}show(){this.viewport.style.display="block"}hide(){this.viewport.style.display="none"}async repaint(t){this.checkCanvas(),this.draw({context:this.ctx,samples:t})}draw({context:t,samples:e}){if(!e||0===e.names.length)return;!function(t,{textAlign:e,textBaseline:i,strokeStyle:n,fillStyle:r},s){const o=Math.min(s,10);t.font=`${o}px sans-serif`,t.textAlign=e,t.textBaseline=i,t.fillStyle=r}(t,ef,e.height),t.clearRect(0,0,t.canvas.width,t.canvas.height),t.fillStyle=function(t){const{r:e,g:i,b:n}=Ko.lead;return`rgb(${e},${i},${n})`}();const i=this.viewport.getBoundingClientRect().height;let n=(e.yOffset||0)+this.contentTop;for(let r of e.names){if(n>i)break;if(n+e.height>0){const i=r,s=rf(t,i,n,e.height);t.fillText(i,4,s)}n+=e.height}}renderSVGContext(t,{deltaX:e,deltaY:i}){if("function"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:s,height:o}=this.viewport.getBoundingClientRect(),a=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_sample_names_guid_${_e.guid()}`;t.saveWithTranslationAndClipRect(a,e,i+r,s,o,-r),this.draw({context:t,samples:n}),t.restore()}}addMouseHandlers(){this.addViewportContextMenuHandler(this.viewport)}removeMouseHandlers(){this.removeViewportContextMenuHandler(this.viewport)}addViewportContextMenuHandler(t){this.boundContextMenuHandler=function(t){t.preventDefault(),t.stopPropagation();const e={label:"Name Panel Width",value:this.browser.sampleNameViewportWidth,callback:t=>{this.browser.sampleNameViewportWidth=parseInt(t);for(let{sampleNameViewport:t}of this.browser.trackViews)t.setWidth(this.browser.sampleNameViewportWidth);this.browser.layoutChange()}};this.browser.inputDialog.present(e,t)}.bind(this),t.addEventListener("contextmenu",this.boundContextMenuHandler)}removeViewportContextMenuHandler(t){t.removeEventListener("contextmenu",this.boundContextMenuHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function rf(t,e,i,n){return i+n-function(t,e,i){const{actualBoundingBoxAscent:n,actualBoundingBoxDescent:r}=t.measureText(e);return(i-(n+r))/2}(t,e,n)}const sf=function(t){this.popover=_e.div({class:"igv-menu-popup"}),t.appendChild(this.popover);const e=_e.div({class:"igv-menu-popup-header"});this.popover.appendChild(e),ki.attachDialogCloseHandlerWithParent(e,(()=>this.hide())),this.popoverContent=_e.div(),this.popover.appendChild(this.popoverContent),Ci(this.popover,e),e.addEventListener("click",(t=>{t.stopPropagation(),t.preventDefault()})),this.hide()};sf.prototype.hide=function(){this.popover.style.display="none"},sf.prototype.presentMenuList=function(t){if(of(),t.length>0){this.popoverContent.innerHTML="",t=Ui.trackMenuItemListHelper(t,this);for(let e of t){e.init&&e.init();let i=e.object;0===t.indexOf(e)&&i.removeClass("igv-track-menu-border-top"),i.hasClass("igv-track-menu-border-top")||i.hasClass("igv-menu-popup-check-container")||i.is("div")&&i.addClass("igv-menu-popup-shim"),this.popoverContent.appendChild(i.get(0))}this.popover.style.display="flex";const{width:e}=this.popover.getBoundingClientRect();this.popover.style.left=-e+"px",this.popover.style.top="0px"}},sf.prototype.presentTrackContextMenu=function(t,e){this.popoverContent.innerHTML="";const i=(n=e,r=this.popover,n.map((t=>{let e;if("string"==typeof t&&"
"===t)e=document.createElement("hr");else if("string"==typeof t)e=_e.div({class:"context-menu"}),e.innerHTML=t;else if("Node"==typeof t)e=t;else{if("function"==typeof t.init&&t.init(),"checkbox"===t.type)e=zi("Show all bases",t.value);else if("color"===t.type){const i=new Pi({parent:r.parentElement,width:364});i.configure(void 0,{color:e=>t.click(e)}),e=_e.div({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);const n=t=>{i.show(),_e.hide(r),t.preventDefault(),t.stopPropagation()};e.addEventListener("click",n),e.addEventListener("touchend",n),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}else e=_e.div({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);if(t.click&&"color"!==t.type){function s(e){t.click(),_e.hide(r),e.preventDefault(),e.stopPropagation()}e.addEventListener("click",s),e.addEventListener("touchend",s),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}}return{el:e,init:t.init}})));var n,r;for(let{el:t}of i)this.popoverContent.appendChild(t);!function(t,e){e.style.display="flex";const{x:i,y:n}=_e.translateMouseCoordinates(t,e.parentNode),{width:r}=e.getBoundingClientRect(),s=i+r,{width:o}=e.parentNode.getBoundingClientRect();e.style.left=`${s>o?i-(s-o):i}px`,e.style.top=`${n}px`}(t,this.popover)},sf.prototype.dispose=function(){this.popoverContent.innerHTML="",this.popover.innerHTML="",Object.keys(this).forEach((function(t){this[t]=void 0}))};const of=()=>{const t=document.querySelectorAll(".igv-menu-popup");for(let e=0;e0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(t,e,i){this.axis=this.createAxis(t,this.track),this.viewports=[];const n=t.calculateViewportWidth(i.length),r=e.querySelectorAll(".igv-column");for(let t=0;t{t.dataRangeDialog.configure(this),t.dataRangeDialog.present(fe(t.columnContainer))}));const{width:n,height:r}=i.getBoundingClientRect();this.axisCanvas=document.createElement("canvas"),this.axisCanvas.style.width=`${n}px`,this.axisCanvas.style.height=`${r}px`,i.appendChild(this.axisCanvas)}return i}resizeAxisCanvas(t,e){this.axis.style.width=`${t}px`,this.axis.style.height=`${e}px`,"function"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${t}px`,this.axisCanvas.style.height=`${e}px`)}removeDOMFromColumnContainer(){this.boundAxisClickHander&&this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.$viewport.remove();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}renderSVGContext(t,{deltaX:e,deltaY:i}){!function(t,e,i,n,r){if("function"==typeof e.paintAxis){const{y:s,width:o,height:a}=i.getBoundingClientRect(),l=`${(e.name||e.id).replace(/\W/g,"")}_axis_guid_${_e.guid()}`;t.saveWithTranslationAndClipRect(l,n,s+r,o,a,0),e.paintAxis(t,o,a),t.restore()}}(t,this.track,this.axisCanvas,e,i);const{width:n}=this.axis.getBoundingClientRect(),{y:r}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let s={deltaX:n+e,deltaY:r+i};for(let e of this.viewports){e.renderSVGContext(t,s);const{width:i}=e.$viewport.get(0).getBoundingClientRect();s.deltaX+=i}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(t,s)}dataRange(){return this.track.dataRange?this.track.dataRange:void 0}setDataRange(t,e){void 0!==t&&(this.track.dataRange.min=t),void 0!==e&&(this.track.dataRange.max=e),this.track.autoscale=!1,this.repaintViews()}presentColorPicker(t){if(!1===lf.has(this.track.type)){const e=[],i=this.track.color||this.track.defaultColor;ji(i)&&e.push(i),this.track.altColor&&ji(this.track.altColor)&&e.push(this.track.altColor);const n=e.map((t=>t.startsWith("#")?t:t.startsWith("rgb(")?xo.rgbToHex(t):xo.colorNameToHex(t))),r={color:t=>{this.track.color=t,this.repaintViews()},altColor:t=>{this.track.altColor=t,this.repaintViews()}};this.browser.genericColorPicker.configure(n,r),this.browser.genericColorPicker.setActiveColorHandler(t),this.browser.genericColorPicker.show()}}setTrackHeight(t,e){e||(this.track.minHeight&&(t=Math.max(this.track.minHeight,t)),this.track.maxHeight&&(t=Math.min(this.track.maxHeight,t))),this.track.height=t,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),"function"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:e}of this.viewports)e.height(t);if(this.sampleNameViewport.viewport.style.height=`${t}px`,"function"!=typeof this.track.computePixelHeight)for(let e of this.viewports)e.setContentHeight(t);this.repaintViews(),!1===af.has(this.track.type)&&this.updateScrollbar(),this.dragHandle.style.height=`${t}px`,this.gearContainer.style.height=`${t}px`}updateScrollbar(){const t=this.viewports[0].$viewport.height();this.outerScroll.style.height=`${t}px`;const e=this.maxViewportContentHeight(),i=Math.round(t/e*t);e>t?(this.innerScroll.style.display="block",this.innerScroll.style.height=`${i}px`):this.innerScroll.style.display="none"}moveScroller(t){const e=fe(this.innerScroll).position().top+t,i=Math.min(Math.max(0,e),this.outerScroll.clientHeight-this.innerScroll.clientHeight);fe(this.innerScroll).css("top",`${i}px`);const n=this.maxViewportContentHeight(),r=-Math.round(i*(n/this.viewports[0].$viewport.height()));for(let t of this.viewports)t.setTop(r);this.sampleNameViewport.trackScrollDelta=t,this.sampleNameViewport.setTop(r)}isLoading(){for(let t of this.viewports)if(t.isLoading())return!0}repaintViews(){for(let t of this.viewports)t.isVisible()&&t.repaint();"function"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSamples()}repaintSamples(){if("function"==typeof this.track.getSamples){const t=this.track.getSamples();this.sampleNameViewport.repaint(t)}}setTrackLabelName(t){this.viewports.forEach((e=>e.setTrackLabel(t)))}resize(t){for(let e of this.viewports)e.setWidth(t)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const t=this.viewports.filter((t=>t.isVisible()));if(t.forEach((t=>t.shift())),this.browser.dragObject)return;const e=t.filter((t=>t.needsRepaint())).filter((t=>t.checkZoomIn())),i=e.filter((t=>t.needsReload()));for(let t of i)await t.loadFeatures();if(this.disposed)return;if(this.track&&"function"==typeof this.track.variantRowCount&&i.length>0){let t=0;for(let e of this.viewports)e.featureCache&&e.featureCache.features&&(t=Math.max(t,e.featureCache.features.reduce(((t,e)=>Math.max(t,e.row||0)),0)));if(this.track.nVariantRows!==t+1){this.track.variantRowCount(t+1);for(let t of this.viewports)t.checkContentHeight()}}if(this.track.autoscale){let e=[];for(let i of t){const t=i.referenceFrame,n=t.start,r=n+t.toBP(i.getWidth());if(i.featureCache&&i.featureCache.features)if("function"==typeof i.featureCache.features.getMax){const t=i.featureCache.features.getMax(n,r);e.push({value:t})}else{const t=Xo(i.featureCache.features,n,r);for(let i of t)e.push(i)}}"function"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(e):this.track.dataRange=ha(e)}const n=this.track.autoscale||this.track.autoscaleGroup||"ruler"===this.track.type;for(let i of t)e.includes(i)?i.repaint():n&&i.refresh();this.adjustTrackHeight(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let t of this.viewports)t.clearCache()}updateRulerViewportLabels(){const t=this.browser.calculateViewportWidth(this.viewports.length);for(let e of this.viewports)"ruler"===this.track.type&&(this.viewports.length>1?e.presentLocusLabel(t):e.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let t=[];const e=this.viewports.filter((t=>t.isVisible()));for(let i of e){const e=i.referenceFrame,{chr:n,start:r,bpPerPixel:s}=i.referenceFrame,o=r+e.toBP(i.getWidth());if((!i.featureCache||!i.featureCache.containsRange(n,r,o,s))&&await i.loadFeatures(),i.featureCache&&i.featureCache.features)if("function"==typeof i.featureCache.features.getMax){const e=i.featureCache.features.getMax(r,o);t.push({value:e})}else{const e="function"==typeof i.featureCache.queryFeatures?i.featureCache.queryFeatures(n,r,o):Xo(i.featureCache.features,r,o);t=t.concat(e)}}return t}checkContentHeight(){for(let t of this.viewports)t.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var t=this.maxViewportContentHeight();if(this.track.autoHeight?this.setTrackHeight(t,!1):this.track.paintAxis&&this.paintAxis(),!1===af.has(this.track.type)){const e=this.viewports[0].getContentTop(),i=this.viewports[0].$viewport.height(),n=Math.min(0,i-t);if(e{t.preventDefault(),void 0===e&&t.target.classList.remove("igv-track-drag-handle-hover")})),this.boundTrackDragMouseOutHandler=s.bind(this),this.dragHandle.addEventListener("mouseout",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){"ideogram"===this.track.id||"ruler"===this.track.id||(this.dragHandle.removeEventListener("mousedown",this.boundTrackDragMouseDownHandler),document.removeEventListener("mouseup",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener("mouseup",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener("mouseout",this.boundTrackDragMouseOutHandler))}addTrackGearMouseHandlers(){if(!0===this.track.ignoreTrackMenu);else{function t(t){t.preventDefault(),t.stopPropagation(),this.trackGearPopup.presentMenuList(Ui.trackMenuItemList(this))}this.boundTrackGearClickHandler=t.bind(this),this.gear.addEventListener("click",this.boundTrackGearClickHandler)}}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener("click",this.boundTrackGearClickHandler)}dispose(){this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.dispose();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),"function"==typeof this.track.dispose&&this.track.dispose();for(let t of Object.keys(this))this[t]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if("function"==typeof this.track.paintAxis){const{width:t,height:e}=this.axisCanvas.getBoundingClientRect(),i=window.devicePixelRatio||1;this.axisCanvas.height=i*e,this.axisCanvas.width=i*t;const n=this.axisCanvas.getContext("2d");n.scale(i,i),this.track.paintAxis(n,t,e)}}maxViewportContentHeight(){return Math.max(this.viewports.map((t=>t.getContentHeight())))}}const cf="rgb(150, 150, 150)";class uf extends ch{static defaults={height:50,flipAxis:!1,logScale:!1,windowFunction:"mean",graphType:"bar",autoscale:!0,normalize:void 0,scaleFactor:void 0};constructor(t,e){super(t,e)}init(t){super.init(t),this.type="wig",this.featureType="numeric",this.paintAxis=$u;const e=t.format?t.format.toLowerCase():t.format;t.featureSource?(this.featureSource=t.featureSource,delete t.featureSource):this.featureSource="bigwig"===e?new Lc(t,this.browser.genome):"tdf"===e?new Dc(t,this.browser.genome):$c(t,this.browser.genome),void 0===t.max||!0===t.autoscale?this.autoscale=!0:this.dataRange={min:t.min||0,max:t.max}}async postInit(){const t=await this.getHeader();this.disposed||t&&this.setTrackProperties(t)}async getFeatures(t,e,i,n){const r=await this.featureSource.getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow,windowFunction:this.windowFunction});if(this.normalize&&this.featureSource.normalizationFactor){const t=this.featureSource.normalizationFactor;for(let e of r)e.value*=t}if(this.scaleFactor){const t=this.scaleFactor;for(let e of r)e.value*=t}return r}menuItemList(){let t=[];return void 0!==this.flipAxis&&(t.push("
"),t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}})),t=t.concat(Ui.numericDataMenuItems(this.trackView)),t}async getHeader(){return"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(t,e,i,n){return n?i/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):i/(e-t)}computeYPixelValue(t,e){return(this.flipAxis?t-this.dataRange.min:this.dataRange.max-t)*e}computeYPixelValueInLogScale(t,e){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),t=Math.log10(t+1),(this.flipAxis?t-n:i-t)*e)}draw(t){const e=t.features,i=t.context,n=t.bpPerPixel,r=t.bpStart,s=t.pixelWidth;t.pixelHeight;const o=r+s*n+1,a=this.color||cf;let l;"string"==typeof a&&a.startsWith("rgb(")&&(l=xo.addAlpha(a,.1));const h=this.getScaleFactor(this.dataRange.min,this.dataRange.max,t.pixelHeight,this.logScale),c=t=>this.logScale?this.computeYPixelValueInLogScale(t,h):this.computeYPixelValue(t,h);if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){let s,a=-1;const h=c(0);for(let t of e){if(t.endo)break;const e=Math.floor((t.start-r)/n);if(isNaN(e))continue;let l=c(t.value);const u=Math.ceil((t.end-r)/n),d=Math.max(1,u-e),f=this.getColorForFeature(t);if("points"===this.graphType){const t=this.config.pointSize||3,n=e+d/2;na.fillCircle(i,n,l,t/2,{fillStyle:f,strokeStyle:f})}else if("line"===this.graphType)null!=s&&na.strokeLine(i,a,s,e,l,{fillStyle:f,strokeStyle:f}),na.strokeLine(i,e,l,e+d,l,{fillStyle:f,strokeStyle:f});else{const t=l-h;na.fillRect(i,e,h,d,t,{fillStyle:f})}a=e+d,s=l}if(this.dataRange.min<0){const e=this.dataRange.max/(this.dataRange.max-this.dataRange.min)*t.pixelHeight;na.strokeLine(i,0,e,t.pixelWidth,e,{strokeStyle:l})}}if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let i=c(e.y),n={strokeStyle:e.color,strokeWidth:2};e.dotted?na.dashedLine(t.context,0,i,t.pixelWidth,i,5,n):na.strokeLine(t.context,0,i,t.pixelWidth,i,n)}}popupData(t,e){if(void 0===e&&(e=this.clickedFeatures(t)),e&&e.length>0){const i=t.genomicLocation,n=[];e.sort((function(t,e){return Math.abs((t.start+t.end)/2-i)-Math.abs((e.start+e.end)/2-i)}));const r=e.length>10?e.slice(0,10):e;r.sort((function(t,e){return t.start-e.start}));for(let t of r)if(t){n.length>0&&n.push("
");let e=t.end-t.start==1?$i(t.start+1):$i(t.start+1)+"-"+$i(t.end);n.push({name:"Position:",value:e}),n.push({name:"Value:     ",value:$i(t.value)})}return r.length..."),n}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}getColorForFeature(t){let e=t.value<0&&this.altColor?this.altColor:this.color||cf;return"function"==typeof e?e(t.value):e}dispose(){this.trackView=void 0}}function df(t){this.thresholds=t.thresholds,this.colors=t.colors}function ff(t){this.scale=t,this.lowColor="rgb("+t.lowR+","+t.lowG+","+t.lowB+")",this.highColor="rgb("+t.highR+","+t.highG+","+t.highB+")",this.diff=t.high-t.low}df.prototype.getColor=function(t){for(let e of this.thresholds)if(t=i.high?this.highColor:(e=(t-i.low)/this.diff,"rgb("+Math.floor(i.lowR+e*(i.highR-i.lowR))+","+Math.floor(i.lowG+e*(i.highG-i.lowG))+","+Math.floor(i.lowB+e*(i.highB-i.lowB))+")")};class pf{constructor(t){this.color=t}getColor(){return this.color}}class gf extends ch{constructor(t,e){super(t,e)}init(t){if(super.init(t),this.type=t.type||"seg","maf"===this.type&&(this.type="mut"),this.isLog=t.isLog,this.displayMode=t.displayMode||"EXPANDED",this.height=t.height||300,this.maxHeight=t.maxHeight||500,this.squishedRowHeight=t.sampleSquishHeight||t.squishedRowHeight||2,this.expandedRowHeight=t.sampleExpandHeight||t.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,t.color?this.color=t.color:(this.posColorScale=t.posColorScale||new ff({low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0}),this.negColorScale=t.negColorScale||new ff({low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255}),"mut"===this.type&&(this.colorTable=new ea(t.colorTable||mf))),this.sampleKeys=[],this.sampleNames=new Map,t.samples){for(let e of t.samples)this.sampleKeys.push(e),this.sampleNames.set(e,e);this.explicitSamples=!0}const e=Object.assign({},this.config);e.maxWGCount=e.maxWGCount||Number.MAX_SAFE_INTEGER,this.featureSource=$c(e,this.browser.genome),this.initialSort=t.sort}async postInit(){"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const t=[],e={SQUISHED:"Squish",EXPANDED:"Expand",FILL:"Fill"};t.push("
"),t.push("DisplayMode:");const i="seg"===this.type?["SQUISHED","EXPANDED","FILL"]:["SQUISHED","EXPANDED"];for(let n of i){const i=zi(e[n],n===this.displayMode);t.push({object:fe(i),click:()=>{this.displayMode=n,this.config.displayMode=n,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return t}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys.map((t=>this.sampleNames.get(t))),height:this.sampleHeight,yOffset:0}}async getFeatures(t,e,i){const n=await this.featureSource.getFeatures({chr:t,start:e,end:i});if(this.initialSort){const t=this.initialSort;this.sortSamples(t.chr,t.start,t.end,t.direction,n),this.initialSort=void 0}return n}draw({context:t,renderSVG:e,pixelTop:i,pixelWidth:n,pixelHeight:r,features:s,bpPerPixel:o,bpStart:a}){if(na.fillRect(t,0,i,n,r,{fillStyle:"rgb(255, 255, 255)"}),s&&s.length>0){this.checkForLog(s),this.updateSampleKeys(s);const e={};let l;switch(this.sampleKeys.forEach((function(t,i){e[t]=i})),this.displayMode){case"FILL":this.sampleHeight=r/this.sampleKeys.length,l=0;break;case"SQUISHED":this.sampleHeight=this.squishedRowHeight,l=0;break;default:this.sampleHeight=this.expandedRowHeight,l=1}const h=this.sampleHeight;for(let t of s)t.pixelRect=void 0;const c=i+r,u=a+n*o+1,d=o;this.sampleYStart=void 0;for(let n of s){if(n.endu)break;const r=n.sampleKey||n.sample;n.row=e[r];const s=n.row*h+l;if(void 0===this.sampleYStart&&(this.sampleYStart=s),s+hc)continue;const o=Math.max(n.start,a);let f=Math.round((o-a)/d);const p=Math.min(n.end,u),g=Math.round((p-a)/d);let m,b,y=Math.max(1,g-f);if(this.color?m="function"==typeof this.color?this.color(n):this.color:this.colorTable&&(m=this.colorTable.getColor(n.value.toLowerCase())),"mut"===this.type)b=h-2*l,y<3&&(y=3,f-=1);else{let t=n.value;this.isLog||(t=vo(t/2)),m=t<-.1?this.negColorScale.getColor(t):t>.1?this.posColorScale.getColor(t):"white";let e=h;if(h<.25){const i=.1+2*Math.abs(t);e=Math.min(1,i*h)}b=e-2*l}n.pixelRect={x:f,y:s,w:y,h:b},t.fillStyle=m,t.fillRect(f,s,y,b)}}}checkForLog(t){if(void 0===this.isLog){this.isLog=!1;for(let e of t)if(e.value<0)return void(this.isLog=!0)}}computePixelHeight(t){if(!t)return 0;const e="SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(t),this.sampleKeys.length*e}async sortSamples(t,e,i,n,r){if(r||(r=await this.featureSource.getFeatures({chr:t,start:e,end:i})),!r)return;this.updateSampleKeys(r);const s={},o="ASC"===n?1:-1;"mut"===this.type?(()=>{for(let t of r){if(t.endi)break;const n=t.sampleKey||t.sample;(!s.hasOwnProperty(n)||t.value.localeCompare(s[n])>0)&&(s[n]=t.value)}this.sampleKeys.sort((function(t,e){let i=s[t]||"",n=s[e]||"";return o*i.localeCompare(n)}))})():(()=>{const t=i-e+1;for(let n of r){if(n.endi)break;const r=Math.max(e,n.start),o=(Math.min(i,n.end)-r)/t,a=n.sampleKey||n.sample,l=s[a]||0;s[a]=l+o*n.value}this.sampleKeys.sort((function(t,e){let i=s[t],n=s[e];return i||(i=o*Number.MAX_VALUE),n||(n=o*Number.MAX_VALUE),i===n?0:i>n?o:-1*o}))})(),this.trackView.repaintViews()}clickedFeatures(t){const e=super.clickedFeatures(t),i=t.y;return e.filter((function(t){const e=t.pixelRect;return e&&i>=e.y&&i<=e.y+e.h}))}hoverText(t){const e=this.clickedFeatures(t);if(e&&e.length>0)return`${e[0].sample}: ${e[0].value}`}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=[];for(let t of e){i.length>0&&(i.push("
"),i.push("
"));const e=t._f||t,n="function"==typeof e.popupData?e.popupData(this.type,this.browser.genome.id):this.extractPopupData(e);Array.prototype.push.apply(i,n)}return i}contextMenuItemList(t){const e=t.viewport.referenceFrame,i=t.genomicLocation,n=this.config.sort?"ASC"===this.config.sort.direction?"DESC":"ASC":"DESC",r=e.toBP(2.5),s=e=>{const i=t.viewport.cachedFeatures;this.sortSamples(e.chr,e.start,e.end,e.direction,i)};return[{label:"seg"===this.type?"Sort by value":"Sort by type",click:e=>{const o={direction:n,chr:t.viewport.referenceFrame.chr,start:i-r,end:i+r};s(o),this.config.sort=o}}]}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(t){if(!this.explicitSamples)for(let e of t){const t=e.sampleKey||e.sample;this.sampleNames.has(t)||(this.sampleNames.set(t,e.sample),this.sampleKeys.push(t))}}}const mf={indel:"rgb(0,200,0)","targeted region":"rgb(236,155,43)",truncating:"rgb(\t150,0,0)","non-coding transcript":"rgb(0,0,150)",synonymous:"rgb(109,165,95)",silent:"rgb(109,135,80)",missense_mutation:"rgb(72,130,187)",missense:"rgb(72,130,187)","splice site":"rgb(143,83,155)",splice_region:"rgb(143,83,155)",nonsense:"rgb(216, 57,81)",nonsense_mutation:"rgb(216, 57,81)",frame_shift_del:"rgb(226,135,65)",frame_shift_ins:"rgb(226,135,65)",in_frame_del:"rgb(247,235,94)",in_frame_ins:"rgb(247,235,94)","*other*":"rgb(159,91,50)"};class bf extends ch{constructor(t,e){super(t,e),this.type="merged",this.featureType="numeric",this.paintAxis=$u,this.graphType=t.graphType}init(t){if(!t.tracks)throw Error("Error: no tracks defined for merged track"+t);super.init(t)}async postInit(){this.tracks=[];const t=[];for(let e of this.config.tracks){e.isMergedTrack=!0;const i=await this.browser.createTrack(e);i?(i.autoscale=!1,this.tracks.push(i)):console.warn("Could not create track "+e),"function"==typeof i.postInit&&t.push(i.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale||void 0===this.config.max,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return this.height=this.config.height||50,Promise.all(t)}get height(){return this._height}set height(t){if(this._height=t,this.tracks)for(let e of this.tracks)e.height=t,e.config.height=t}menuItemList(){let t=[];return void 0!==this.flipAxis&&t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),t=t.concat(Ui.numericDataMenuItems(this.trackView)),t}async getFeatures(t,e,i,n){const r=this.tracks.map((r=>r.getFeatures(t,e,i,n))),s=await Promise.all(r);return new yf(s)}draw(t){const e=t.features;for(let i=0,n=this.tracks.length;i0&&i.push("
"),i.push(`
${this.tracks[n].name}
`);const r=this.tracks[n].popupData(t,e[n]);i.push(...r)}return i}}}clickedFeatures(t){const e=t.viewport.cachedFeatures;if(!e)return[];const i=t.genomicLocation,n=[];for(let r of e.featureArrays){const e=t.referenceFrame.bpPerPixel>.2?3*t.referenceFrame.bpPerPixel:.2,s=Xo(r,i-e,i+e);for(let t of s)n.push(t)}return n}get supportsWholeGenome(){return this.tracks.every((t=>t.supportsWholeGenome))}}class yf{constructor(t){this.featureArrays=t}getMax(t,e){let i=-Number.MAX_VALUE;for(let n of this.featureArrays)for(let r of n)if(void 0!==r.value&&!Number.isNaN(r.value)){if(r.ende)break;i=Math.max(i,r.value)}return i}}class vf extends ch{static defaults={height:250,theta:Math.PI/4,arcOrientation:!0,showBlocks:!0,blockHeight:3,thickness:1,alpha:.02,logScale:!0};constructor(t,e){super(t,e)}init(t){super.init(t),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.arcType=function(t){if(!t.arcType)return"nested";switch(t.arcType){case"chiapet":return"inView";case"chiapetoutbound":return"partialInView";default:return t.arcType}}(t),this.alpha=t.alpha||.02,this.painter={flipAxis:!this.arcOrientation,dataRange:this.dataRange,paintAxis:$u},t.valueColumn?(this.valueColumn=t.valueColumn,this.hasValue=!0):t.useScore&&(this.hasValue=!0,this.valueColumn="score"),t.max?(this.dataRange={min:t.min||0,max:t.max},this.autoscale=!1):this.autoscale=!0,t.featureSource?(this.featureSource=t.featureSource,delete t._featureSource):(this.featureSource=$c(t,this.browser.genome),this.featureSource.getWGFeatures=Sf)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,i){const n=this.visibilityWindow,r=await this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:n});return void 0===this.hasValue&&r&&r.length>0&&(this.hasValue=void 0!==r[0].score),r}draw(t){"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?this.drawProportional(t):this.drawNested(t)}drawNested(t){const e=t.context,i=t.pixelWidth,n=t.pixelHeight,r=t.viewportWidth,s=t.bpPerPixel,o=t.bpStart,a=s;na.fillRect(e,0,t.pixelTop,i,n,{fillStyle:"rgb(255, 255, 255)"});const l=t.features;if(l){(function(){let t=0;for(let e of l){let n=(e.start-o)/a,r=(e.end-o)/a;n>=0&&r<=i&&(t=Math.max(t,r-n))}let e=Math.min(r,t)/2;if(t>0){let t=(n-10)/e;this.theta=function(t){let e,i=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],n=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(e=0;et);e++);let r=0===e?0:i[e-1],s=(t-r)/((ei)continue;let f=d-u;f<3&&(f=3,u--);const p=f/2,g=p/this.sinTheta,m=this.cosTheta*g,b=u+p;let y,v,w;if(c?(y=this.height+m,v=Math.PI+Math.PI/2-this.theta,w=Math.PI+Math.PI/2+this.theta):(y=-m,v=Math.PI/2-this.theta,w=Math.PI/2+this.theta),this.showBlocks&&"all"!==t.chr){const i=(t.start1-o)/a,n=(t.end1-o)/a,r=(t.start2-o)/a,l=(t.end2-o)/a,h=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(i,s,n-i,h),e.fillRect(r,s,l-r,h)}n&&!this.config.useScore&&f>r&&(n=kf(n,this.alpha)),e.strokeStyle=n,e.fillStyle=n,e.beginPath(),e.arc(b,y,g,v,w,!1),e.stroke(),t.drawState={xc:b,yc:y,r:g}}else{let r=Math.round((t.start-o)/a),s=Math.round((t.end-o)/a);if(s<0||r>i)continue;let l=s-r;l<3&&(l=3,r--);const h=t.chr===t.chr1?t.chr2:t.chr1;e.strokeStyle=n,e.fillStyle=kf(Zd(h),.5),c?(e.fillRect(r,this.height/2,l,this.height/2),e.fillText(h,r+l/2,this.height/2-5),t.drawState={x:r,y:this.height/2,w:l,h:this.height/2}):(e.fillRect(r,0,l,this.height/2),e.fillText(h,r+l/2,this.height/2+13),t.drawState={x:r,y:0,w:l,h:this.height/2})}}}var h}getScaleFactor(t,e,i,n){return n?i/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):i/(e-t)}drawProportional(t){const e=t.context,i=t.pixelWidth,n=t.pixelHeight,r=t.bpPerPixel,s=t.bpStart,o=r,a=t.referenceFrame.start,l=t.referenceFrame.end;na.fillRect(e,0,t.pixelTop,i,n,{fillStyle:"rgb(255, 255, 255)"});const h=t.features;if(h&&h.length>0){const n=0,r=this.getScaleFactor(n,this.dataRange.max,t.pixelHeight-1,this.logScale),c=this.arcOrientation?t.pixelHeight:0;for(let t of h){t.drawState=void 0;const n=this.valueColumn?t[this.valueColumn]:t.score;if(void 0===n||Number.isNaN(n))continue;const h=Math.round((this.logScale?Math.log10(n+1):n)*r);if(t.chr1===t.chr2||"all"===t.chr){const{m1:i,m2:r}=wf(t,this.browser.genome);let u=Math.round((i-s)/o),d=Math.round((r-s)/o)-u;if(d<3&&(d=3,u--),nthis.dataRange.max)continue;if("proportional"!==this.arcType){const t="partialInView"===this.arcType,e=i>=a&&r<=l;let n=!1,s=!1;if(!e&&t&&(n=a<=i&&i<=l,n||(s=a<=r&&r<=l)),!(e||n||s))continue}const f=d/2,p=u+d/2;t.drawState={xc:p,yc:c,radiusX:f,radiusY:h};const g=!!this.arcOrientation,m=t.color||this.color;if(e.strokeStyle=m,e.lineWidth=t.thickness||this.thickness||1,!0===e.isSVG?e.strokeEllipse(p,c,f,h,0,0,Math.PI,g):(e.beginPath(),e.ellipse(p,c,f,h,0,0,Math.PI,g),e.stroke()),this.alpha&&(e.fillStyle=kf(m,this.alpha),!0===e.isSVG?e.fillEllipse(p,c,f,h,0,0,Math.PI,g):e.fill()),this.showBlocks&&"all"!==t.chr){e.fillStyle=m;const i=(t.start1-s)/o,n=(t.end1-s)/o,r=(t.start2-s)/o,a=(t.end2-s)/o,l=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(i,c,n-i,l),e.fillRect(r,c,a-r,l)}}else{let r=Math.round((t.start-s)/o),a=Math.round((t.end-s)/o);if(a<0||r>i||nthis.dataRange.max)continue;const l=Math.min(h,this.height-13);let c=a-r;c<3&&(c=3,r--);const u=t.chr===t.chr1?t.chr2:t.chr1;if(e.font="8px sans-serif",e.textAlign="center",e.fillStyle=kf(Zd(u),.5),this.arcOrientation){const i=this.height-l;e.fillRect(r,i,c,l),e.fillText(u,r+c/2,i-5),t.drawState={x:r,y:i,w:c,h:l}}else e.fillRect(r,0,c,l),e.fillText(u,r+c/2,l+13),t.drawState={x:r,y:0,w:c,h:l}}}}}clearAxis(t,e,i){na.fillRect(t,0,0,e,i,{fillStyle:"rgb(255, 255, 255)"})}paintAxis(t,e,i){const n={min:0,max:this.dataRange.max};"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?(this.painter.flipAxis=!this.arcOrientation,this.painter.dataRange=n,this.painter.paintAxis(t,e,i)):this.clearAxis(t,e,i)}menuItemList(){let t=[];if(this.hasValue){t.push("
");const e={nested:"Nested",proportional:"Proportional - All",inView:"Proportional - Both Ends in View",partialInView:"Proportional - One End in View"};t.push("Arc Type");for(let i of["nested","proportional","inView","partialInView"])t.push({object:fe(zi(e[i],i===this.arcType)),click:()=>{this.arcType=i,this.trackView.repaintViews()}})}return t.push("
"),t.push({name:"Toggle arc direction",click:()=>{this.arcOrientation=!this.arcOrientation,this.trackView.repaintViews()}}),t.push({name:this.showBlocks?"Hide Blocks":"Show Blocks",click:()=>{this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),"proportional"!==this.arcType&&"inView"!==this.arcType&&"partialInView"!==this.arcType||(t=t.concat(Ui.numericDataMenuItems(this.trackView))),this.browser.circularView&&(t.push("
"),t.push({label:"Add interactions to circular view",click:()=>{for(let t of this.trackView.viewports)this.addChordsForViewport(t.referenceFrame)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,i=[];return i.push({label:"Add interactions to circular view",click:()=>{const t=e.referenceFrame;this.addChordsForViewport(t)}}),i.push("
"),i}}addChordsForViewport(t){const e=("all"===t.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end)).filter((t=>t.drawState));0!==e.length&&_d(e.map((t=>{const e=t._f||t;return{uniqueId:`${e.chr1}:${e.start1}-${e.end1}_${e.chr2}:${e.start2}-${e.end2}`,refName:vd(e.chr1),start:e.start1,end:e.end1,mate:{refName:vd(e.chr2),start:e.start2,end:e.end2}}})),this,t,.5)}doAutoscale(t){let e=0;if(t)for(let i of t){const t=this.valueColumn?i[this.valueColumn]:i.score;Number.isNaN(t)||(e=Math.max(e,t))}return{min:0,max:e}}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=[];for(let t of e){const e=t._||t;if(i.push({name:"Region 1",value:_f(e.chr1,e.start1,e.end1,e.strand1)}),i.push({name:"Region 2",value:_f(e.chr2,e.start2,e.end2,e.strand2)}),e.name&&i.push({name:"Name",value:e.name}),void 0!==e.value&&i.push({name:"Value",value:e.value}),void 0!==e.score&&i.push({name:"Score",value:e.score}),e.extras&&this.header&&this.header.columnNames){const t=this.header.columnNames,n=this.header.hiccups?6:10;for(let r=n;r=e-a&&t.canvasX<=e+s+a&&t.canvasY>=n&&t.canvasY<=n+o){const n=-Math.abs(t.canvasX-(e+s/2));i.push({score:n,feature:r});break}}}return i.length>1&&i.sort(((t,e)=>t.score-e.score)),i.map((t=>t.feature))}}function wf(t,e){let i=(t.start1+t.end1)/2,n=(t.start2+t.end2)/2;if("all"===t.chr&&(i=e.getGenomeCoordinate(t.chr1,i),n=e.getGenomeCoordinate(t.chr2,n)),i>n){const t=i;i=n,n=t}return{m1:i,m2:n}}function _f(t,e,i,n){return n&&"."!==n?`${t}:${$i(e+1)}-${$i(i)} (${n})`:`${t}:${$i(e+1)}-${$i(i)}`}const xf=new Map;function kf(t,e){const i=`${t}_${e}`;let n=xf.get(i);return n||(n=xo.addAlpha(t,e),xf.set(i,n)),n}function Sf(t){const e=t=>{const e=Object.assign({},t);return e.chr="all",e.start=i.getGenomeCoordinate(t.chr1,t.start1),e.end=i.getGenomeCoordinate(t.chr2,t.end2),e},i=this.genome;let n,r=0;for(let e of i.wgChromosomeNames){let i=t[e];if(i)for(let t of i)t.dup||(r++,t.score&&(!n||t.score>n.score)&&(n=t))}const s=this.maxWGCount,o=n&&n.score>0&&r>s?5:1,a=Math.floor(s/o),l=n&&n.score>0?Math.log(n.score)/o:Number.MAX_SAFE_INTEGER;let h,c=[],u=[];for(let t=0;tt.name)):[]}return this.header}getCallsetsLength(){return this.callSets?this.callSets.length:0}async getFeatures(t,e,i,n){return void 0===this.header&&(this.header=await this.getHeader()),this.featureSource.getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow})}hasSamples(){return this.getCallsetsLength()>0}getSamples(){return{yOffset:this.sampleYOffset,names:this.sampleNames,height:this.sampleHeight}}computePixelHeight(t){if(!t||0==t.length)return 10;const e="COLLAPSED"===this.displayMode?1:this.nVariantRows,i="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,n="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,r="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight;return 10+e*(n+i)+i+(1+(!1===this.showGenotypes?0:this.getCallsetsLength()*e))*(r+i)}variantRowCount(t){this.nVariantRows=t}draw({context:t,pixelWidth:e,pixelHeight:i,bpPerPixel:n,bpStart:r,pixelTop:s,features:o}){na.fillRect(t,0,s,e,i,{fillStyle:"rgb(255, 255, 255)"});const a="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,l="COLLAPSED"===this.displayMode?1:this.nVariantRows,h="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=10+l*(h+a);let c=this.callSets;!c&&this._f&&(c=this._f.callSets);const u=this.getCallsetsLength();if(c&&u>0&&!1!==this.showGenotypes&&na.strokeLine(t,0,this.variantBandHeight,e,this.variantBandHeight,{strokeStyle:"rgb(224,224,224) "}),o){const i="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,a=r+e*n+1;for(let e of o){if(e.enda)break;const o="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,l=10+("COLLAPSED"===this.displayMode?0:e.row*(o+s)),h=o;let d=Math.round((e.start-r)/n),f=Math.round((e.end-r)/n),p=Math.max(1,f-d);p<3?(p=3,d-=1):p>5&&(d+=1,p-=2),t.fillStyle=this.getColorForFeature(e),t.fillRect(d,l,p,h);let g=this.getVariantStrokecolor(e);if(g&&(t.strokeStyle=g,t.strokeRect(d,l,p,h)),this.callContextHook(e,t,d,l,p,h),e.pixelRect={x:d,y:l,w:p,h},u>0&&!1!==this.showGenotypes){const n="COLLAPSED"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+s,this.sampleHeight=n*(i+s);let r=0;if(c&&e.calls)for(let n of c){const o=e.calls[n.id];if(o){const a="COLLAPSED"===this.displayMode?0:e.row,l=this.sampleYOffset+r*this.sampleHeight+a*(i+s);let h=!0,c=!0,u=!1;if(o.genotype)for(let t of o.genotype){if("."===t){u=!0;break}0!==t&&(c=!1),0===t&&(h=!1)}o.genotype?t.fillStyle=u?this.noCallColor:c?this.homrefColor:h?this.homvarColor:this.hetvarColor:t.fillStyle=this.noGenotypeColor,t.fillRect(d,l,p,i),n.pixelRect={x:d,y:l,w:p,h:i}}r++}}}}else console.log("No feature list")}getColorForFeature(t){const e=t._f||t;let i;if(this.colorBy){const t=this.colorBy;let n;e.info.hasOwnProperty(t)?n=e.info[t]:Tf.has(t)&&(n=e[Tf.get(t)]),i=this.getVariantColorTable(t).getColor(n),i||(i="gray")}else i=this._color?"function"==typeof this._color?this._color(t):this._color:"NONVARIANT"===e.type?this.nonRefColor:"MIXED"===e.type?this.mixedColor:this.color;return i}getVariantStrokecolor(t){const e=t._f||t;let i;return i=this._strokecolor?"function"==typeof this._strokecolor?this._strokecolor(e):this._strokecolor:void 0,i}callContextHook(t,e,i,n,r,s){if(this._context_hook&&"function"==typeof this._context_hook){const o=t._f||t;e.save(),this._context_hook(o,e,i,n,r,s),e.restore()}}clickedFeatures(t){let e=super.clickedFeatures(t);const i="EXPANDED"===this.displayMode?this.expandedVGap:this.squishedVGap,n=i+("SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),r=t.y;if(r<=this.variantBandHeight){const t="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=Math.floor((r-10)/(t+i));"COLLAPSED"!==this.displayMode&&(e=e.filter((t=>t.row===n)))}else if(this.callSets){const t=this.callSets,i=r-this.variantBandHeight,s=Math.floor(i/this.sampleHeight);if(s>=0&&st.row===r)),a=t[s];e=o.map((t=>{const e=t.calls[a.id];return function(t,e){if(t.genotype){let i="";if("."===e.alternateBases)i="No Call";else{const n=e.alternateBases.split(",");for(let r of t.genotype)i.length>0&&(i+="|"),i+="."===r?".":0===r?e.referenceBases:n[r-1].replace("<","<")}t.genotypeName=i}}(e,t),e}))}}return e}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=t.genomicLocation,n=this.browser.genome.id,r=this.browser.sampleInformation;let s=[];for(let t of e){const e=t._f||t;if(s.length>0&&s.push({html:'
'}),"function"==typeof e.popupData){const t=e.popupData(i,n);Array.prototype.push.apply(s,t)}else{const t=e;if(void 0!==t.callSetName&&s.push({name:"Name",value:t.callSetName}),t.genotypeName&&s.push({name:"Genotype",value:t.genotypeName}),void 0!==t.phaseset&&s.push({name:"Phase set",value:t.phaseset}),void 0!==t.genotypeLikelihood&&s.push({name:"genotypeLikelihood",value:t.genotypeLikelihood.toString()}),r){var o=r.getAttributes(t.callSetName);o&&Object.keys(o).forEach((function(t){var e=t.replace(/([A-Z])/g," $1");e=e.charAt(0).toUpperCase()+e.slice(1),s.push({name:e,value:o[t]})}))}var a=Object.keys(t.info);a.length&&s.push("
"),a.forEach((function(e){s.push({name:e,value:decodeURIComponent(t.info[e])})}))}}return s}menuItemList(){const t=[];if(this.header.INFO&&this.header.INFO){const e=this.header.INFO.SVTYPE?["SVTYPE"]:[];if(this._initColorBy&&"SVTYPE"!==this._initColorBy&&e.push(this._initColorBy),e.length>0){t.push("
");const i=fe('
');i.text("Color by:"),t.push({name:void 0,object:i,click:void 0,init:void 0}),e.sort();for(let i of e){const e=this.colorBy===i,n=i||"None";t.push(this.colorByCB({key:i,label:n},e))}t.push(this.colorByCB({key:void 0,label:"None"},void 0===this.colorBy)),t.push("
")}}this.getCallsetsLength()>0&&(t.push({object:fe('
')}),t.push({object:fe(zi("Show Genotypes",this.showGenotypes)),click:()=>{this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),t.push({object:fe('
')});for(let e of["COLLAPSED","SQUISHED","EXPANDED"])t.push({object:fe(zi({COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"}[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}});return this.browser.circularView&&(t.push("
"),t.push({label:"Add SVs to circular view",click:()=>{for(let t of this.trackView.viewports)this.sendChordsForViewport(t)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,i=[];return i.push({label:"Add SVs to Circular View",click:()=>{this.sendChordsForViewport(e)}}),i.push("
"),i}}sendChordsForViewport(t){const e=t.referenceFrame;let i;if("all"===e.chr){const t=this.featureSource.getAllFeatures(),e=Object.keys(t).map((e=>t[e]));i=[].concat(...e)}else i=this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end);_d(i.filter((t=>{const e=t._f||t;return e.info&&e.info.CHR2&&e.info.END&&(e.info.CHR2!==e.chr||Math.abs(Number.parseInt(e.info.END)-e.pos)>1e6)})).map((t=>{const e=t._f||t,i=Number.parseInt(e.info.END),n=i-100,r=i+100;return{uniqueId:`${e.chr}:${e.start}-${e.end}_${e.info.CHR2}:${e.info.END}`,refName:vd(e.chr),start:e.start,end:e.end,mate:{refName:vd(e.info.CHR2),start:n,end:r}}})),this,e,.5)}colorByCB(t,e){return{name:void 0,object:fe(zi(t.label,e)),click:()=>{t.key===this.colorBy?(this.colorBy=void 0,delete this.config.colorBy,this.trackView.repaintViews()):(this.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews())},init:void 0}}getState(){const t=super.getState();return this._color&&"function"!=typeof this._color&&(t.color=this._color),t}getVariantColorTable(t){if(this.colorTables||(this.colorTables=new Map),!this.colorTables.has(t)){let e;e="SVTYPE"===t?Ef:new ta("Set1"),this.colorTables.set(t,e)}return this.colorTables.get(t)}}const Ef=new ea({DEL:"#ff2101",INS:"#001888",DUP:"#028401",INV:"#008688",CNV:"#8931ff",BND:"#891100","*":"#002eff"});class Mf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.name=t.name,this.pValueField=t.pValueField||"pValue",this.geneField=t.geneField||"geneSymbol",this.snpField=t.snpField||"snp";const e=t.minLogP||t.min,i=t.maxLogP||t.max;this.dataRange={min:e||3.5,max:i||25},this.autoscale=!i||t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||2,this.height=t.height||100,this.autoHeight=!1,this.disableButtons=t.disableButtons,this.visibilityWindow=void 0===t.visibilityWindow?2e6:t.visibilityWindow>=0?Math.min(2e6,t.visibilityWindow):2e6,this.featureSource=$c(t,this.browser.genome),Sd.gtexLoaded=!0}paintAxis(t,e,i){const n=(this.dataRange.max-this.dataRange.min)/i,r={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};na.fillRect(t,0,0,e,i,{fillStyle:"rgb(255, 255, 255)"});const s=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let o=4;o<=this.dataRange.max;o+=s){const s=.85*e,a=s-5,l=s,h=i-(o-this.dataRange.min)/n;na.strokeLine(t,a,h,l,h,r),h>8&&na.fillText(t,o,a-1,h+2,r)}r.textAlign="center",na.fillText(t,"-log10(pvalue)",e/4,i/2,r,{rotate:{angle:-90}})}async getFeatures(t,e,i){const n=this.pValueField,r=this.visibilityWindow,s=await this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:r});return s.forEach((function(t){t.value=t[n]})),s}draw(t){const e=t.context,i=t.pixelWidth,n=t.pixelHeight;this.background&&na.fillRect(e,0,0,i,n,{fillStyle:this.background}),na.strokeLine(e,0,n-1,i,n-1,{strokeStyle:this.divider});const r=r=>{const s=r?2*this.dotSize:this.dotSize,o=t.bpStart,a=(this.dataRange.max-this.dataRange.min)/n,l=t.referenceFrame.selection;for(let c of t.features){const u=(c.start-o+.5)/t.bpPerPixel;if(u<0)continue;if(u>i)break;const d=c.snp.toUpperCase(),f=c[this.geneField].toUpperCase(),p=l&&(l.snp===d||l.gene===f);if(!r||p){l&&l.snp===d&&l.addGene(f);var h=-Math.log(c[this.pValueField])/Math.LN10;if(h>=this.dataRange.min){let t;h>this.dataRange.max?(h=this.dataRange.max,t=!0):t=!1;const i=Math.max(0+s,n-Math.round((h-this.dataRange.min)/a));let o;c.px=u,c.py=i,c.radius=s,r&&l?(o=l.colorForGene(f),na.setProperties(e,{fillStyle:o,strokeStyle:"black"})):(o=t?"rgb(150, 150, 150)":"rgb(180, 180, 180)",na.setProperties(e,{fillStyle:o,strokeStyle:o})),na.fillCircle(e,u,i,s),na.strokeCircle(e,u,i,s)}}}};r(!1),r(!0)}popupData(t,e){if(void 0===e&&(e=t.viewport.cachedFeatures),!e||0===e.length)return[];const i=this.name,n=[];for(let r of e)Math.abs(r.px-t.canvasX)0&&n.push("
"),n.push({name:"snp id",value:r.snp},{name:"gene id",value:r.geneId},{name:"gene name",value:r.geneName},{name:"p value",value:r.pValue},{name:"tissue",value:i}));return n}menuItemList(){return Ui.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){var e=t.map((function(t){return-Math.log(t.value)/Math.LN10}));this.dataRange.max=function(t,e){if(0!==t.length){var i=Math.floor(t.length*((100-e)/100));return 0===i?(t.sort((function(t,e){return e-t})),t[i]):function(t,e){var i,n=new wo;for(i=0;in.content[0])&&(n.content.length===e&&n.pop(),n.push(r))}return n.content[0]}(t,i)}}(e,this.autoscalePercentile)}else{const t=this.config.maxLogP||this.config.max;this.dataRange.max=t||25}return this.dataRange}}const Rf={X:"rgb(204, 153, 0)",Y:"rgb(153, 204, 0)",Un:"darkGray)",1:"rgb(80, 80, 255)",2:"rgb(206, 61, 50)","2a":"rgb(210, 65, 55)","2b":"rgb(215, 70, 60)",3:"rgb(116, 155, 88)",4:"rgb(240, 230, 133)",5:"rgb(70, 105, 131)",6:"rgb(186, 99, 56)",7:"rgb(93, 177, 221)",8:"rgb(128, 34, 104)",9:"rgb(107, 215, 107)",10:"rgb(213, 149, 167)",11:"rgb(146, 72, 34)",12:"rgb(131, 123, 141)",13:"rgb(199, 81, 39)",14:"rgb(213, 143, 92)",15:"rgb(122, 101, 165)",16:"rgb(228, 175, 105)",17:"rgb(59, 27, 83)",18:"rgb(205, 222, 183)",19:"rgb(97, 42, 121)",20:"rgb(174, 31, 99)",21:"rgb(231, 199, 111)",22:"rgb(90, 101, 94)",23:"rgb(204, 153, 0)",24:"rgb(153, 204, 0)",25:"rgb(51, 204, 0)",26:"rgb(0, 204, 51)",27:"rgb(0, 204, 153)",28:"rgb(0, 153, 204)",29:"rgb(10, 71, 255)",30:"rgb(71, 117, 255)",31:"rgb(255, 194, 10)",32:"rgb(255, 209, 71)",33:"rgb(153, 0, 51)",34:"rgb(153, 26, 0)",35:"rgb(153, 102, 0)",36:"rgb(128, 153, 0)",37:"rgb(51, 153, 0)",38:"rgb(0, 153, 26)",39:"rgb(0, 153, 102)",40:"rgb(0, 128, 153)",41:"rgb(0, 51, 153)",42:"rgb(26, 0, 153)",43:"rgb(102, 0, 153)",44:"rgb(153, 0, 128)",45:"rgb(214, 0, 71)",46:"rgb(255, 20, 99)",47:"rgb(0, 214, 143)",48:"rgb(20, 255, 177)"};for(let Sy of Object.keys(Rf))Rf["chr"+Sy]=Rf[Sy];for(let Cy=1;Cy<=48;Cy++){if(10===Cy)continue;const Ay=Lf(Cy);Rf[Ay]=Rf[Cy.toString()]}function Lf(t){if(!+t)return!1;for(var e=String(+t).split(""),i=["","C","CC","CCC","CD","D","DC","DCC","DCCC","CM","","X","XX","XXX","XL","L","LX","LXX","LXXX","XC","","I","II","III","IV","V","VI","VII","VIII","IX"],n="",r=3;r--;)n=(i[+e.pop()+10*r]||"")+n;return Array(+e.join("")+1).join("M")+n}class Bf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.useChrColors=void 0===t.useChrColors||t.useChrColors,this.trait=t.trait,this.posteriorProbability=t.posteriorProbability,this.valueProperty="bed"===t.format?"score":"value",this.height=t.height||100,this.autoscale=t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||3,this.popoverWindow=void 0===t.popoverWindow?1e8:t.popoverWindow,this.useChrColors?this.colorScale=new ea(t.colorTable||Rf):t.color?this.colorScale=new pf(t.color):this.colorScale=new df(t.colorScale||{thresholds:[5e-8,5e-4,.5],colors:["rgb(255,50,50)","rgb(251,100,100)","rgb(251,170,170)","rgb(227,238,249)"]}),this.featureSource=$c(t,this.browser.genome)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:n})}draw(t){const e=t.features,i=t.context,n=t.pixelWidth,r=t.pixelHeight;if(this.background&&na.fillRect(i,0,0,n,r,{fillStyle:this.background}),na.strokeLine(i,0,r-1,n,r-1,{strokeStyle:this.divider}),e){const s=t.bpPerPixel,o=t.bpStart,a=o+n*s+1;for(let t of e){const e=t.start;if(ea)break;let n;if(this.posteriorProbability)n=t[this.valueProperty];else{const e=t[this.valueProperty];if(!e)continue;n=-Math.log10(e)}const l=this.useChrColors?t._f?t._f.chr:t.chr:n,h=this.colorScale.getColor(l),c=(this.dataRange.max-this.dataRange.min)/r,u=Math.round((e-o)/s),d=Math.max(this.dotSize,r-Math.round((n-this.dataRange.min)/c));h&&na.setProperties(i,{fillStyle:h,strokeStyle:"black"}),na.fillCircle(i,u,d,this.dotSize),t.px=u,t.py=d}}}paintAxis(t,e,i){na.fillRect(t,0,0,e,i,{fillStyle:"rgb(255, 255, 255)"});var n={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};const r=(this.dataRange.max-this.dataRange.min)/i;if(this.posteriorProbability){const e=.1;for(let s=this.dataRange.min;s0&&i.push("
"),5==r){i.push("...");break}if("function"==typeof s.popupData)i=i.concat(s.popupData());else{const t=s.realChr||s.chr,e=(s.realStart||s.start)+1;i.push({name:"chromosome",value:t}),i.push({name:"position",value:e}),i.push({name:"name",value:s.name}),n.posteriorProbability?i.push({name:"posterior probability",value:a}):i.push({name:"pValue",value:a})}r++}}}return i}menuItemList(){return Ui.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){const e=this.valueProperty,i=this.posteriorProbability,n=t.map((function(t){const n=t[e];return{value:i?n:-Math.log(n)/Math.LN10}}));this.dataRange=ha(n)}else this.posteriorProbability?this.dataRange={min:this.config.min||0,max:this.config.max||1}:this.dataRange={min:this.config.max||25,max:this.config.min||0};return this.dataRange}}class Nf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.autoscale=t.autoscale||void 0===t.max,this.dataRange={min:t.min||0,max:t.max},this.windowFunction=t.windowFunction||"mean",this.paintAxis=$u,this.graphType=t.graphType||"bar",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=$c(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if("function"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleNames=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty("clickToHighlight")){let t=this.header.clickToHighlight;this.config.clickToHighlight=t,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty("highlight")){this.config.highlightSamples={};let t=this.header.highlight;Array.isArray(t)||(t=[t]);for(let e of t){const t=e.split(";");2===t.length&&(this.config.highlightSamples[t[0]]=t[1])}}}}menuItemList(){return Ui.numericDataMenuItems(this.trackView)}async getFeatures(t,e,i){const n=await this.featureSource.getFeatures({chr:t,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let r,s;for(let t=1;te&&(r=t-1),void 0===s&&n[t].start>i){s=t+1;break}return void 0===r&&(r=0),void 0===s&&(s=n.length),n.slice(r,s)}draw(t){const{features:e,context:i,bpPerPixel:n,bpStart:r,pixelWidth:s,pixelHeight:o}=t,a=t=>(this.dataRange.max-t)/(this.dataRange.max-this.dataRange.min)*o,l=function(t){let e=Math.floor((t-r)/n);return isNaN(e)&&console.warn("isNaN(x). feature start "+$i(t)+" bp start "+$i(r)),e};if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const t=this.config.highlightSamples,n=this.config.onlyHandleClicksForHighlightedSamples,r=this.config.clickToHighlight;let s=-1,o={},h=[],c=[];this.clickDetectorCache={};for(let u of e){const e=l(u.start),d=l(u.end),f=s>=0?l(s):e;if(!isNaN(e)&&!isNaN(d)){this.clickDetectorCache[e]=[],this.clickDetectorCache[d]=[];for(let s=0;s=1){const s=o[l],c=a(s),u=t&&t[l];u?h.push([f,c,e,g,u]):r&&l in this.config.samplesClickedToHighlight?h.push([f,c,e,g,this.config.samplesClickedToHighlight[l]]):na.strokeLine(i,f,c,e,g,{strokeStyle:"#D9D9D9"}),n&&!(l in t)||this.clickDetectorCache[e].push([f,c,e,g,l,u||"gray"])}if(d-e>=1){const s=t&&t[l];s?c.push([e,g,d,g,s]):r&&l in this.config.samplesClickedToHighlight?c.push([e,g,d,g,this.config.samplesClickedToHighlight[l]]):na.strokeLine(i,e,g,d,g,{strokeStyle:"gray"}),n&&!(l in t)||this.clickDetectorCache[d].push([e,g,d,g,l,s||"gray"])}o[l]=p}s=u.end}}for(let t of h)na.strokeLine(i,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:1.3});for(let t of c)na.strokeLine(i,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:2})}(t=>{if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let i=a(e.y),n={strokeStyle:e.color,strokeWidth:2};e.dotted?na.dashedLine(t.context,0,i,t.pixelWidth,i,5,n):na.strokeLine(t.context,0,i,t.pixelWidth,i,n)}})(t)}doAutoscale(t){let e,i;return t.length>0?(e=Number.MAX_VALUE,i=-Number.MAX_VALUE,t.forEach((function(t){e=Math.min(e,...t.values),i=Math.max(i,...t.values)})),e-=.01,i+=.01):(e=0,i=100),{min:e,max:i}}clickedFeatures(t){const e=t.canvasX,i=t.canvasY;let n=null;for(n of Object.keys(this.clickDetectorCache))if(n=parseInt(n),n>=e)break;if(n){let t=Number.MAX_VALUE,o=[];const a=this.clickDetectorCache[n];for(let n of a){const r=n[0],s=n[2];if(es)return[];const a=n[1],l=n[3];if(iMath.max(a,l)+10)continue;const h=Ff(e,i,r,a,s,l);h0?l/h:0}class Of extends ch{constructor(t,e){super(t,e),t.height||(this.height=300),this.arcOrientation=!1,this.theta=Math.PI/2,"bp"===t.format?this.featureSource=new Pf(t,e.genome):this.featureSource=new bc(t,e.genome)}async getFeatures(t,e,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:n})}draw(t){const e=t.context,i=Math.PI/2,n=t.pixelWidth,r=t.pixelHeight;t.viewportWidth;const s=t.bpPerPixel,o=t.bpStart,a=s,l=this.arcOrientation;na.fillRect(e,0,t.pixelTop,n,r,{fillStyle:"rgb(255, 255, 255)"});const h=t.features;if(h){Df(h,1);for(let t of h)if(t.startLeft){let n=Math.round((t.startLeft-o)/a),r=Math.round((t.startRight-o)/a),s=Math.round((t.endLeft-o)/a),h=Math.round((t.endRight-o)/a);e.fillStyle=t.color,e.strokeStyle=t.color,e.beginPath();let c=(n+h)/2,u=(h-n)/2,d=this.height,f=Math.PI+(Math.PI/2-i),p=2*Math.PI-(Math.PI/2-i);l?(d=0,e.arc(c,d,u,p,f),e.lineTo(h,d)):(e.arc(c,d,u,f,p),e.lineTo(s,d));const g=(r+s)/2,m=(s-r)/2,b=d;l?(e.arc(g,b,m,f,p,!0),e.lineTo(s,b)):(e.arc(g,b,m,p,f,!0),e.lineTo(n,b)),e.stroke(),e.fill(),t.drawState={x1:c,y1:d,r1:u,x2:g,y2:b,r2:m,sa:f,ea:p}}else{let n=Math.round((t.start-o)/a),r=Math.round((t.end-o)/a);e.strokeStyle=t.color,e.beginPath();let s=(n+r)/2,h=(r-n)/2,c=this.height,u=Math.PI+(Math.PI/2-i),d=2*Math.PI-(Math.PI/2-i);l?(c=0,e.arc(s,c,h,d,u)):e.arc(s,c,h,u,d),e.stroke(),t.drawState={x1:s,y1:c,r1:h,sa:u,ea:d}}}}clickedFeatures(t){const e=super.clickedFeatures(t),i=[];Df(e,-1);for(let n of e){const e=n.drawState,r=t.canvasX-e.x1,s=t.canvasY-e.y1,o=Math.sqrt(r*r+s*s),a=e.r1+3;let l,h;if(void 0===e.x2)l=o,h=e.r1-3;else{const i=t.canvasX-e.x2,n=t.canvasY-e.y2;l=Math.sqrt(i*i+n*n),h=e.r2-3}if(oh){i.push(n);break}}return i}popupData(t,e){if(void 0===e&&(e=this.clickedFeatures(t)),e&&e.length>0)return this.extractPopupData(e[0],this.getGenomeId())}menuItemList(){var t=this;return[{name:"Toggle arc direction",click:function(){t.arcOrientation=!t.arcOrientation,t.trackView.repaintViews()}}]}}function Df(t,e){t.sort((function(t,i){const n=void 0===t.score?-Number.MAX_VALUE:t.score,r=void 0===i.score?-Number.MAX_VALUE:i.score;return(void 0===e?1:e)*(n-r)}))}class Pf{constructor(t,e){this.config=t,this.genome=e}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(t,e,i);{const n=la(this.config),r=await zo.loadString(this.config.url,n);return this.featureCache=new Zo(function(t){if(!t)return null;const e=Hh(t);let i,n=!0;const r=[],s=[],o=[];for(;void 0!==(i=e.nextLine());){const t=i.split("\t");if(n&&i.startsWith("color:")){const e="rgb("+t[1]+","+t[2]+","+t[3]+")";r.push(e),t.length>4&&s.push(t[4])}else{n=!1;const e=t[0],i=Number.parseInt(t[1])-1,l=Number.parseInt(t[2])-1,h=Number.parseInt(t[3]),c=Number.parseInt(t[4]);var a=Number.parseInt(t[5]);const u=r[a];let d;d=i<=c?{chr:e,startLeft:Math.min(i,l),startRight:Math.max(i,l),endLeft:Math.min(h,c),endRight:Math.max(h,c),color:u,score:a}:{chr:e,startLeft:Math.min(h,c),startRight:Math.max(h,c),endLeft:Math.min(i,l),endRight:Math.max(i,l),color:u,score:a},d.start=d.startLeft,d.end=d.endRight,s.length>a&&(d.description=s[a]),o.push(d)}}return o}(r),s),this.featureCache.queryFeatures(t,e,i)}}}class zf{constructor(t){this.browser=t,this.type="ideogram",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}async getFeatures(t,e,i){return[]}computePixelHeight(t){return this.height}draw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n}){const r=e.chr,s=e.genome.getChromosome(r);if(void 0===s||i<=0||n<=0||"all"===r.toLowerCase())return;!function({ctx:t,chr:e,referenceFrame:i,genome:n,width:r,height:s,stainColors:o}){const a=.5;if(void 0===n)return;na.fillRect(t,0,0,r,s,{fillStyle:xo.greyScale(255)});const l=n.getCytobands(e);if(l){const e=0+s/2,i=[],n=[];if(0===l.length)return;const h=r/l[l.length-1].end;t.beginPath(),na.roundRect(t,a,.5,r-1,s-1,(s-1)/2,0,1),t.clip();for(let r=0;r0&&h[h.length-1].end&&(l=Math.max(l,h[h.length-1].end),s.bpLength=l),o{Vf.getColor(t)}));const Hf={};class jf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.type=t.type||"junctions",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=t.featureSource?t.featureSource:$c(t,this.browser.genome),this.margin=void 0===t.margin?10:t.margin,this.height||(this.height=100),void 0===t.colorByNumReadsThreshold&&(t.colorByNumReadsThreshold=5)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return!1}async getFeatures(t,e,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(t){return this.height}draw(t){const e=t.features,i=t.context,n=t.bpPerPixel,r=t.bpStart,s=t.pixelWidth,o=t.pixelHeight,a=r+s*n+1;if(this.config.isMergedTrack||na.fillRect(i,0,t.pixelTop,s,o,{fillStyle:"rgb(255, 255, 255)"}),e){Hf.referenceFrame=t.viewport.referenceFrame,Hf.referenceFrameStart=Hf.referenceFrame.start,Hf.referenceFrameEnd=Hf.referenceFrameStart+Hf.referenceFrame.toBP(t.viewport.getWidth()),Hf.featureZoomOutTracker={};for(let t of e)if(!(t.enda)break;this.renderJunction(t,r,n,o,i)}}else console.log("No feature list")}renderJunction(t,e,i,n,r){t.isVisible=!1;const s=Math.round((t.start-e)/i),o=Math.round((t.end-e)/i),a=(s+o)/2;if(o-s<=3){if(a in Hf.featureZoomOutTracker)return;Hf.featureZoomOutTracker[a]=!0}if(this.config.hideAnnotatedJunctions&&"true"===t.attributes.annotated_junction)return;if(this.config.hideUnannotatedJunctions&&"false"===t.attributes.annotated_junction)return;if(this.config.hideMotifs&&this.config.hideMotifs.includes(t.attributes.motif))return;if(this.config.hideStrand===t.strand)return;if(this.config.minJunctionEndsVisible){let e=0;if(t.start>=Hf.referenceFrameStart&&t.start<=Hf.referenceFrameEnd&&(e+=1),t.end>=Hf.referenceFrameStart&&t.end<=Hf.referenceFrameEnd&&(e+=1),e0&&h/c>this.config.maxFractionMultiMappedReads)return;if(t.attributes.maximum_spliced_alignment_overhang&&parseInt(t.attributes.maximum_spliced_alignment_overhang)this.config.maxSamplesWithThisJunction)return;if(t.attributes.num_samples_total&&(t.attributes.percent_samples_with_this_junction=100*u/Number(t.attributes.num_samples_total),this.config.minPercentSamplesWithThisJunction&&(t.attributes.percent_samples_with_this_junctionthis.config.maxPercentSamplesWithThisJunction)))return}const d=this.margin,f=this.height,p=d+.5*f;let g=d;const m=d+f-10,b=(s+a)/2,y=(a+o)/2;let v,w,_=1;t.attributes.line_width?_=Number(t.attributes.line_width):(void 0===this.config.thicknessBasedOn||"numUniqueReads"===this.config.thicknessBasedOn?_=l:"numReads"===this.config.thicknessBasedOn?_=c:"numSamplesWithThisJunction"===this.config.thicknessBasedOn&&void 0!==u&&(_=u),_=1+Math.log(_+1)/Math.log(12)),void 0===this.config.bounceHeightBasedOn||"random"===this.config.bounceHeightBasedOn?v=(t.start+t.end)%7:"distance"===this.config.bounceHeightBasedOn?v=6*(t.end-t.start)/(Hf.referenceFrameEnd-Hf.referenceFrameStart):"thickness"===this.config.bounceHeightBasedOn&&(v=2*_),g+=f*Math.max(7-v,0)/10,w=t.attributes.color?t.attributes.color:void 0===this.config.colorBy||"numUniqueReads"===this.config.colorBy?l>this.config.colorByNumReadsThreshold?"blue":"#AAAAAA":"numReads"===this.config.colorBy?c>this.config.colorByNumReadsThreshold?"blue":"#AAAAAA":"isAnnotatedJunction"===this.config.colorBy?"true"===t.attributes.annotated_junction?"#b0b0ec":"orange":"strand"===this.config.colorBy?"+"===t.strand?"#b0b0ec":"#ecb0b0":"motif"===this.config.colorBy?Vf.getColor(t.attributes.motif):"#AAAAAA";let x="";t.attributes.label?x=t.attributes.label.replace(/_/g," "):void 0===this.config.labelWith||"uniqueReadCount"===this.config.labelWith?x=l:"totalReadCount"===this.config.labelWith?x=c:"numSamplesWithThisJunction"===this.config.labelWith?void 0!==u&&(x=u):"percentSamplesWithThisJunction"===this.config.labelWith?void 0!==t.attributes.percent_samples_with_this_junction&&(x=t.attributes.percent_samples_with_this_junction.toFixed(0)+"%"):"motif"===this.config.labelWith&&void 0!==t.attributes.motif&&(x+=t.attributes.motif),"uniqueReadCount"===this.config.labelWithInParen?x+=" ("+l+")":"totalReadCount"===this.config.labelWithInParen?x+=" ("+c+")":"multiMappedReadCount"===this.config.labelWithInParen?h>0&&(x+=" (+"+h+")"):"numSamplesWithThisJunction"===this.config.labelWithInParen?void 0!==u&&(x+=" ("+u+")"):"percentSamplesWithThisJunction"===this.config.labelWithInParen?void 0!==t.attributes.percent_samples_with_this_junction&&(x+=" ("+t.attributes.percent_samples_with_this_junction.toFixed(0)+"%)"):"motif"===this.config.labelWithInParen&&void 0!==t.attributes.motif&&(x+=` ${t.attributes.motif}`),t.isVisible=!0,r.beginPath(),r.moveTo(s,m),r.bezierCurveTo(b,g,y,g,o,m),r.lineWidth=_,r.strokeStyle=w,r.stroke();const k=(t,e,i,n)=>{t.beginPath(),t.moveTo(e,i),t.lineTo(e-n/2,i-n),t.lineTo(e+n/2,i-n),t.lineTo(e,i),t.closePath(),t.fill()};if(t.attributes.left_shape||t.attributes.right_shape){r.fillStyle=w;const e=r.lineWidth>2?10:7;t.attributes.left_shape&&k(r,s,m,e),t.attributes.right_shape&&k(r,o,m,e)}r.fillText(x,a-r.measureText(x).width/2,(7*g+p)/8)}clickedFeatures(t){return super.clickedFeatures(t).filter((function(t){return t.isVisible&&t.attributes}))}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=t.genomicLocation,n=[];for(let t of e){const e="function"==typeof t.popupData?t.popupData(i):this.extractPopupData(t._f||t,this.getGenomeId());e&&(n.length>0&&n.push("

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jp;i=t.state,i.mode===Zp&&(i.mode=13),o=t.next_out,r=t.output,l=t.avail_out,s=t.next_in,n=t.input,a=t.avail_in,h=i.hold,c=i.bits,u=a,d=l,k=Up;t:for(;;)switch(i.mode){case 1:if(0===i.wrap){i.mode=13;break}for(;c<16;){if(0===a)break t;a--,h+=n[s++]<>>8&255,i.check=xp(i.check,C,2,0),h=0,c=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&h)<<8)+(h>>8))%31){t.msg="incorrect header check",i.mode=Yp;break}if((15&h)!==Gp){t.msg="unknown compression method",i.mode=Yp;break}if(h>>>=4,c-=4,x=8+(15&h),0===i.wbits)i.wbits=x;else if(x>i.wbits){t.msg="invalid window size",i.mode=Yp;break}i.dmax=1<>8&1),512&i.flags&&(C[0]=255&h,C[1]=h>>>8&255,i.check=xp(i.check,C,2,0)),h=0,c=0,i.mode=3;case 3:for(;c<32;){if(0===a)break t;a--,h+=n[s++]<>>8&255,C[2]=h>>>16&255,C[3]=h>>>24&255,i.check=xp(i.check,C,4,0)),h=0,c=0,i.mode=4;case 4:for(;c<16;){if(0===a)break t;a--,h+=n[s++]<>8),512&i.flags&&(C[0]=255&h,C[1]=h>>>8&255,i.check=xp(i.check,C,2,0)),h=0,c=0,i.mode=5;case 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t;a--,h+=n[s++]<>>16^65535)){t.msg="invalid stored block lengths",i.mode=Yp;break}if(i.length=65535&h,h=0,c=0,i.mode=15,e===zp)break t;case 15:i.mode=16;case 16:if(f=i.length,f){if(f>a&&(f=a),f>l&&(f=l),0===f)break t;r.set(n.subarray(s,s+f),o),a-=f,s+=f,l-=f,o+=f,i.length-=f;break}i.mode=Zp;break;case 17:for(;c<14;){if(0===a)break t;a--,h+=n[s++]<>>=5,c-=5,i.ndist=1+(31&h),h>>>=5,c-=5,i.ncode=4+(15&h),h>>>=4,c-=4,i.nlen>286||i.ndist>30){t.msg="too many length or distance symbols",i.mode=Yp;break}i.have=0,i.mode=18;case 18:for(;i.have>>=3,c-=3}for(;i.have<19;)i.lens[I[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,A={bits:i.lenbits},k=Op(0,i.lens,0,19,i.lencode,0,i.work,A),i.lenbits=A.bits,k){t.msg="invalid code lengths set",i.mode=Yp;break}i.have=0,i.mode=19;case 19:for(;i.have>>24,b=S>>>16&255,y=65535&S,!(m<=c);){if(0===a)break t;a--,h+=n[s++]<>>=m,c-=m,i.lens[i.have++]=y;else{if(16===y){for(T=m+2;c>>=m,c-=m,0===i.have){t.msg="invalid bit length 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21:if(a>=6&&l>=258){t.next_out=o,t.avail_out=l,t.next_in=s,t.avail_in=a,i.hold=h,i.bits=c,Rp(t,d),o=t.next_out,r=t.output,l=t.avail_out,s=t.next_in,n=t.input,a=t.avail_in,h=i.hold,c=i.bits,i.mode===Zp&&(i.back=-1);break}for(i.back=0;S=i.lencode[h&(1<>>24,b=S>>>16&255,y=65535&S,!(m<=c);){if(0===a)break t;a--,h+=n[s++]<>v)],m=S>>>24,b=S>>>16&255,y=65535&S,!(v+m<=c);){if(0===a)break t;a--,h+=n[s++]<>>=v,c-=v,i.back+=v}if(h>>>=m,c-=m,i.back+=m,i.length=y,0===b){i.mode=26;break}if(32&b){i.back=-1,i.mode=Zp;break}if(64&b){t.msg="invalid literal/length code",i.mode=Yp;break}i.extra=15&b,i.mode=22;case 22:if(i.extra){for(T=i.extra;c>>=i.extra,c-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;S=i.distcode[h&(1<>>24,b=S>>>16&255,y=65535&S,!(m<=c);){if(0===a)break t;a--,h+=n[s++]<>v)],m=S>>>24,b=S>>>16&255,y=65535&S,!(v+m<=c);){if(0===a)break t;a--,h+=n[s++]<>>=v,c-=v,i.back+=v}if(h>>>=m,c-=m,i.back+=m,64&b){t.msg="invalid distance code",i.mode=Yp;break}i.offset=y,i.extra=15&b,i.mode=24;case 24:if(i.extra){for(T=i.extra;c>>=i.extra,c-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){t.msg="invalid distance too far back",i.mode=Yp;break}i.mode=25;case 25:if(0===l)break t;if(f=d-l,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){t.msg="invalid distance too far back",i.mode=Yp;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>l&&(f=l),l-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=21);break;case 26:if(0===l)break t;r[o++]=i.length,l--,i.mode=21;break;case 27:if(i.wrap){for(;c<32;){if(0===a)break t;a--,h|=n[s++]<{if(!t||!t.state)return jp;let e=t.state;return e.window&&(e.window=null),t.state=null,Up},inflateGetHeader:(t,e)=>{if(!t||!t.state)return jp;const i=t.state;return 0==(2&i.wrap)?jp:(i.head=e,e.done=!1,Up)},inflateSetDictionary:(t,e)=>{const i=e.length;let n,r,s;return t&&t.state?(n=t.state,0!==n.wrap&&11!==n.mode?jp:11===n.mode&&(r=1,r=wp(r,e,i,0),r!==n.check)?$p:(s=og(t,e,i,i),s?(n.mode=31,qp):(n.havedict=1,Up))):jp},inflateInfo:"pako inflate (from Nodeca project)"},lg=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name="",this.comment="",this.hcrc=0,this.done=!1},hg=Object.prototype.toString,{Z_NO_FLUSH:cg,Z_FINISH:ug,Z_OK:dg,Z_STREAM_END:fg,Z_NEED_DICT:pg,Z_STREAM_ERROR:gg,Z_DATA_ERROR:mg,Z_MEM_ERROR:bg}=Sp;function yg(t){this.options=Ap.assign({chunkSize:65536,windowBits:15,to:""},t||{});const e=this.options;e.raw&&e.windowBits>=0&&e.windowBits<16&&(e.windowBits=-e.windowBits,0===e.windowBits&&(e.windowBits=-15)),!(e.windowBits>=0&&e.windowBits<16)||t&&t.windowBits||(e.windowBits+=32),e.windowBits>15&&e.windowBits<48&&0==(15&e.windowBits)&&(e.windowBits|=15),this.err=0,this.msg="",this.ended=!1,this.chunks=[],this.strm=new Mp,this.strm.avail_out=0;let i=ag.inflateInit2(this.strm,e.windowBits);if(i!==dg)throw new Error(kp[i]);if(this.header=new lg,ag.inflateGetHeader(this.strm,this.header),e.dictionary&&("string"==typeof e.dictionary?e.dictionary=Ep.string2buf(e.dictionary):"[object ArrayBuffer]"===hg.call(e.dictionary)&&(e.dictionary=new Uint8Array(e.dictionary)),e.raw&&(i=ag.inflateSetDictionary(this.strm,e.dictionary),i!==dg)))throw new Error(kp[i])}function vg(t,e){const i=new yg(e);if(i.push(t),i.err)throw i.msg||kp[i.err];return i.result}yg.prototype.push=function(t,e){const i=this.strm,n=this.options.chunkSize,r=this.options.dictionary;let s,o,a;if(this.ended)return!1;for(o=e===~~e?e:!0===e?ug:cg,"[object ArrayBuffer]"===hg.call(t)?i.input=new Uint8Array(t):i.input=t,i.next_in=0,i.avail_in=i.input.length;;){for(0===i.avail_out&&(i.output=new Uint8Array(n),i.next_out=0,i.avail_out=n),s=ag.inflate(i,o),s===pg&&r&&(s=ag.inflateSetDictionary(i,r),s===dg?s=ag.inflate(i,o):s===mg&&(s=pg));i.avail_in>0&&s===fg&&i.state.wrap>0&&0!==t[i.next_in];)ag.inflateReset(i),s=ag.inflate(i,o);switch(s){case gg:case mg:case pg:case bg:return this.onEnd(s),this.ended=!0,!1}if(a=i.avail_out,i.next_out&&(0===i.avail_out||s===fg))if("string"===this.options.to){let t=Ep.utf8border(i.output,i.next_out),e=i.next_out-t,r=Ep.buf2string(i.output,t);i.next_out=e,i.avail_out=n-e,e&&i.output.set(i.output.subarray(t,t+e),0),this.onData(r)}else this.onData(i.output.length===i.next_out?i.output:i.output.subarray(0,i.next_out));if(s!==dg||0!==a){if(s===fg)return s=ag.inflateEnd(this.strm),this.onEnd(s),this.ended=!0,!0;if(0===i.avail_in)break}}return!0},yg.prototype.onData=function(t){this.chunks.push(t)},yg.prototype.onEnd=function(t){t===dg&&("string"===this.options.to?this.result=this.chunks.join(""):this.result=Ap.flattenChunks(this.chunks)),this.chunks=[],this.err=t,this.msg=this.strm.msg};var wg={Inflate:yg,inflate:vg,inflateRaw:function(t,e){return(e=e||{}).raw=!0,vg(t,e)},ungzip:vg,constants:Sp},{Inflate:_g,inflate:xg,inflateRaw:kg,ungzip:Sg}=wg,Cg=xg,Ag=Sg,Tg=new Map([[1,function(t,e){let i=new Uint8Array(t);return Cg(i).buffer}],[2,function(t,e){let i=t.byteLength,n=new Uint8Array(i),r=Math.floor(i/e),s=new DataView(t);for(var o=0;oHH",t,i);if(r!=(a%=65535)||s!=(l%=65535))throw'ValueError("fletcher32 checksum invalid")'}(t),t.slice(0,-4)}]]),Ig=class{constructor(t,e){this.fh=t,this.offset=e,this.depth=null}async init(){this.all_nodes=new Map,await this._read_root_node(),await this._read_children()}async _read_children(){let t=this.depth;for(;t>0;){for(var e of this.all_nodes.get(t))for(var i of e.get("addresses"))this._add_node(await this._read_node(i,t-1));t--}}async _read_root_node(){let t=await this._read_node(this.offset,null);this._add_node(t),this.depth=t.get("node_level")}_add_node(t){let e=t.get("node_level");this.all_nodes.has(e)?this.all_nodes.get(e).push(t):this.all_nodes.set(e,[t])}async _read_node(t,e){let i=await this._read_node_header(t,e);return i.set("keys",[]),i.set("addresses",[]),i}async _read_node_header(t){throw"NotImplementedError: must define _read_node_header in implementation class"}},Eg=class extends Ig{B_LINK_NODE=new Map([["signature","4s"],["node_type","B"],["node_level","B"],["entries_used","H"],["left_sibling","Q"],["right_sibling","Q"]]);async _read_node_header(t,e){let i=await Zf(this.B_LINK_NODE,this.fh,t);if(null!=e&&i.get("node_level")!=e)throw"node level does not match";return i}},Mg=class extends Eg{NODE_TYPE=0;constructor(t,e){super(t,e),this.ready=this.init()}async _read_node(t,e){let i=await this._read_node_header(t,e);t+=Xf(this.B_LINK_NODE);let n=[],r=[],s=i.get("entries_used");for(var o=0;o=0&&v[x]>=t[x];x--)v[x]=0,y[x]=b[x],x>0&&(v[x-1]+=1,y[x-1]+=1);if(y.slice(0,-1).every((function(t,i){return t=0;o--){if(e&1<0?r*=n:r=n}}return s}_nrecords_max(t,e,i){return Math.floor((t-10-i)/(e+i))}_required_bytes(t){return Math.ceil(np(t)/8)}_int_format(t){return["0&&(c=(await ep.unpack_from_async(a,this.fh,i))[0],i+=r),l.push([n,h,c])}}return s.set("keys",a),s.set("addresses",l),s}async _read_node_header(t,e){let i=await Zf(this.B_LINK_NODE,this.fh,t);return i.set("node_level",e),i}*iter_records(){for(let t of this.all_nodes.values())for(let e of t)for(let t of e.get("keys"))yield t}_parse_record(t){throw"NotImplementedError"}},Bg=class extends Lg{NODE_TYPE=5;async _parse_record(t,e,i){let n=(await ep.unpack_from_async("0)throw"Filter info size not supported on FractalHeap";if(e.get("btree_address_huge_objects")!=Vg)throw"Huge objects not implemented in FractalHeap";e.set("btree_address_huge_objects",null),e.get("root_block_address")==Vg&&e.set("root_block_address",null);let i=e.get("log2_maximum_heap_size"),n=this._min_size_nbits(i),r=new Map([["signature","4s"],["version","B"],["heap_header_adddress","Q"],["block_offset",`${n}B`]]);this.indirect_block_header=new Map(r),this.indirect_block_header_size=Xf(r),2==(2&e.get("flags"))&&r.set("checksum","I"),this.direct_block_header=r,this.direct_block_header_size=Xf(r);let s=e.get("maximum_direct_block_size");this._managed_object_offset_size=this._min_size_nbits(i);let o=Math.min(s,e.get("max_managed_object_size"));this._managed_object_length_size=this._min_size_integer(o);let a=e.get("starting_block_size"),l=e.get("table_width");if(!(a>0))throw"Starting block size == 0 not implemented";let h=Number(Math.floor(Math.log2(s)));Qf(1n<0)for await(let t of this._iter_indirect_block(this.fh,f,p))d.push(t);else{let t=await this._read_direct_block(this.fh,f,a);d.push(t)}let g=d.reduce(((t,e)=>t+e.byteLength),0),m=new Uint8Array(g),b=0;d.forEach((t=>{m.set(new Uint8Array(t),b),b+=t.byteLength})),this.managed=m.buffer}async _read_direct_block(t,e,i){let n=await t.slice(e,e+i);return Qf("FHDB"==Yf(this.direct_block_header,n).get("signature")),n}get_data(t){let e=ep.unpack_from(">4&3,n=1;if(0==i){Qf(0==e>>6);let i=this._managed_object_offset_size,r=rp(i,t,n);n+=i,i=this._managed_object_length_size;let s=rp(i,t,n);return this.managed.slice(r,r+s)}throw 1==i?"tiny objectID not supported in FractalHeap":2==i?"huge objectID not supported in FractalHeap":"unknown objectID type in FractalHeap"}_min_size_integer(t){return this._min_size_nbits(np(t))}_min_size_nbits(t){return Math.ceil(t/8)}async*_iter_indirect_block(t,e,i){let n=await Zf(this.indirect_block_header,t,e);e+=this.indirect_block_header_size,Qf("FHIB"==n.get("signature"));let r=n.get("block_offset").reduce(((t,e,i)=>t+(e<<8*i)),0);n.set("block_offset",r);let[s,o]=this._indirect_info(i),a=[];for(let i=0;ithis._chunks))}get shape(){let t=this.find_msg_type(Im)[0].get("offset_to_message");return async function(t,e){let i=(await ep.unpack_from_async("255&&(s=(await ep.unpack_from_async("0;t.set("optional",a);let l,h=(await ep.unpack_from_async("0&&(l=(await ep.unpack_from_async(`${s}s`,i,e))[0],e+=s),t.set("name",l);let c=await ep.unpack_from_async(`<${h}i`,i,e);e+=4*h,t.set("client_data_values",c),r.push(t)}}return this._filter_pipeline=r,this._filter_pipeline}find_msg_type(t){return this.msgs.filter((function(e){return e.get("type")==t}))}async get_attributes(){let t={},e=this.find_msg_type(Fm);for(let i of e){let e=i.get("offset_to_message"),[n,r]=await this.unpack_attribute(e);t[n]=r}return t}async get_fillvalue(){var t,e=this.find_msg_type(Rm)[0].get("offset_to_message");let i=(await ep.unpack_from_async("=r&&([s,r]=a[++l],h=0);let e=await Zf(gm,t,s+h),i=s+h+mm;if(e.set("offset_to_message",i),e.get("type")==Om){var[d,f]=await ep.unpack_from_async("=o-ym){let t=l[++h];if(null==t)break;[r,o]=t,c=0}let e=await Zf(bm,t,r+c),i=r+c+ym+n;if(e.set("offset_to_message",i),e.get("type")==Om){var[u,d]=await ep.unpack_from_async("0,l=(4&n)>0;(8&n)>0?(r=(await ep.unpack_from_async("0&&(e+=8);let r=(2&n)>0?_m:wm,s=await Zf(r,t,e),o=new Map;for(let[t,e]of s.entries())o.set(t,e==nm?null:e);return o}get is_dataset(){return this.find_msg_type(Im).length>0}async get_data(){let t=this.find_msg_type(Bm)[0].get("offset_to_message");var[e,i,n,r]=await this._get_data_message_properties(t);if(0==n)throw"Compact storage of DataObject not implemented";return 1==n?this._get_contiguous_data(r):2==n?this._get_chunked_data(t):void 0}async _get_data_message_properties(t){let e,i,n,[r,s,o]=await ep.unpack_from_async("=1&&r<=4),[r,e,i,n]}async _get_contiguous_data(t){let[e]=await ep.unpack_from_async("=!@\|]?(i|u|f|S)(\d*)/.test(n)){let[t,i,s]=tp(n),a=new Array(r);const l=await this.fh.slice(e,e+s*r);let h=new ip(l);for(var o=0;o=1&&e<=3);var a="<"+(i-1).toFixed()+"I",l=await ep.unpack_from_async(a,this.fh,s);this._chunks=l,this._chunk_dims=i,this._chunk_address=o}}}},nm=ep.unpack_from("this.get(t)))}length(){return this.keys.length}_dereference(t){if(!t)throw"cannot deference null reference";let e=this.file._get_object_by_address(t);if(null==e)throw"reference not found in file";return e}async get(t){if("number"==typeof t)return this._dereference(t);var e=Vm(t);if("/"==e)return this.file;if("."==e)return this;if(/^\//.test(e))return this.file.get(e.slice(1));if(""!=function(t){let e=t.lastIndexOf("/")+1,i=t.slice(0,e),n=new RegExp("^/+$"),r=new RegExp("/$");return i&&!n.test(i)&&(i=i.replace(r,"")),i}(e))var[i,n]=e.split(/\/(.*)/);else var i=e,n=".";if(!(i in this._links))throw i+" not found in group";var r=Vm(this.name+"/"+i);let s=this._links[i];if("string"==typeof s)try{return this.get(s)}catch(t){return null}var o=new im(this.file._fh,s);if(await o.ready,o.is_dataset){if("."!=n)throw r+" is a dataset, not a group";return new Um(r,o,this)}var a=new Pm(r,this);return await a.init(o),a.get(n)}visit(t){return this.visititems(((e,i)=>t(e)))}visititems(t){var e=this.name.length;/\/$/.test(this.name)||(e+=1);for(var i=this.values.slice();i;){let n=i.shift();1==i.length&&console.log(n);let r=t(n.name.slice(e),n);if(null!=r)return r;n instanceof Pm&&(i=i.concat(n.values))}return null}get attrs(){return null==this._attrs&&(this._attrs=this._dataobjects.get_attributes()),this._attrs}},zm=class extends Pm{constructor(t,e,i){super("/",null),this.ready=this.init(t,e,i)}async init(t,e,i){var n=new Fg(t,0);await n.ready;var r=await n.get_offset_to_dataobjects(),s=new im(t,r);if(await s.ready,this.parent=this,this.file=this,this.name="/",this._dataobjects=s,this._attrs=null,this._keys=null,this._fh=t,this.filename=e||"",this.mode="r",this.userblock_size=0,i&&i.index)this.index=i.index;else{let e;if(i&&i.indexOffset)e=i.indexOffset;else{const t=await 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b=Gm(o,1,m),y={},v={};for(let t=10;t>-1;t--)for(let e=0;e1-e+e*t/2)),a=t/2;t>0?(n=.5-e/(e+s),r=b.map(((t,i)=>.5-(1-t+t*e)/(2-2*t+(e+s)*t)))):(n=0,r=b.map(((t,e)=>0*t)));for(let i=0;i{if(!isNaN(r[e])){let n=nb(t*this.globalMean,1,d[i],f[i])*ab(p[i],.5+r[e]);h+=n,n>c&&(c=n,u=b[e])}})),i in y?y[i].push([t,e,s,h/b.length,u]):y[i]=[t,e,s,h/b.length,u]}for(let t=0;tt[3]-e[3]));else if(y[t].sort(((t,e)=>t[3]-e[3])),"both"==i&&(v[t].sort(((t,e)=>t[3]-e[3])),v[t][0][3]>y[t][0][3])){let e=y[t].filter((e=>e[0]!=v[t][0][0]&&e[1]<=v[t][0][1]));y[t]=[v[t][0]].push(...e)}for(let t=0;t{var r={...t};1!=i&&(r.value=t[e]/i*2),n.push(r)}));return n}formatDataStructure_BAF(t,e=2){const i=[],n=[];for(const[e,r]of Object.entries(this.wigFeatures))r.forEach((e=>{var r={...e},s={...e};let o=e[t];.5!=o&&(s.value=-2*(1-o),n.push(s)),r.value=-2*o,i.push(r)}));return[i,n]}};function cb(t){for(var e=1,i=1,n=1*t,r=1;r<50;r++)e*=r,n+=(i*=-1)*Math.pow(t,2*r+1)/(e*(2*r+1));return 2*n/Math.sqrt(3.14159265358979)}function ub(t,e,i,n,r){var s=new pb(i.slice(n,r));return 0==s.std&&(s.std=e>0?e*s.mean/t:1),gb(t,s.mean,s.std,r-n)/(r-n)}function db(t,e,i,n,r){var s=new pb(i.slice(n,r));if(s.means&!h&l0&&(c=ub(t,e,i,n-1,r)),r-n>2)var u=ub(t,e,i,n+1,r),d=ub(t,e,i,n,r-1);if(rt+e))/t.length,this.std=Math.sqrt(t.reduce(((t,e)=>(e-this.mean)**2))/t.length)}}function gb(t,e,i,n){0==i&&(i=1);var r=(t-e)/i*Math.sqrt(n);return 1-eb.TdistributionCDF(Math.abs(r),n-1)}function mb(t,e,i,n,r,s){0==e&&(e=1),0==r&&(r=1);var o=(t-n)/Math.sqrt(e**2/i+r**2/s),a=(e**2/i+r**2/s)**2*(i-1)*(s-1)/(e**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-eb.TdistributionCDF(Math.abs(o),parseInt(a+.5))}var bb=class{constructor(t,e,i){this.rd=t,this.mean=e,this.std=i,this.bin_bands=[2,3,4,5,6,7,8,10,12,14,16,20,24,28,32,40,48,56,64,80,96,112,128]}get_rd_signal_bandwidth(t){var e=[];return t.forEach(((t,i)=>{var n;n=t>this.mean/4?this.mean/(this.std**2*t):4/this.std**2,e.push(n)})),e}meanShiftCaller(t=3){var e={};return Object.entries(this.rd).forEach((([i,n])=>{var r=new Array(n.length).fill(!1),s=new Array(n.length);for(let t=0;t{var o=r.map(((t,e)=>!t)),a=[];Object.entries(n).forEach((([t,e])=>{a.push(e.binScore)}));var l=[0],h=0;for(let t=0;t0&&(l.push(l[l.length-1]+h-1),h=0):h+=1;l.shift();for(let i=0;i=a.length||Math.abs(t-i)>=a.length)){var d=(i-t)*Math.exp(-.5*(i-t)**2/e**2)*Math.exp(-.5*(a[t]-a[i])**2*c[t]);u[t]+=d}for(var f=new Array,p=0;p=0&&f.push(p);f.push(u.length-1),f=f.concat(l).sort(((t,e)=>t-e)),f=Array.from(new Set(f));var g=0;for(p=0;pt+e))/m.length;a.fill(b,g,f[p]+1),g=f[p]+1}}p=0;for(var y=0;p.01&&f.push(p+1);for(f.unshift(0),f.push(s.length),r=new Array(this.rd.length).fill(!1),p=1;p1))continue;w[0]=f[p-2];var _=[f[p],f[p]];if(!(p.01/genome_size*bin_size*(x+k))continue;if(mb(C.mean,C.std,C.data.length,M.mean,M.std,M.data.length)>.01/genome_size*bin_size*(x+S))continue}if(gb(this.mean,C.mean,C.std,C.data.length)>.05)continue;let t=a.slice(v[0],v[1]);var R=new pb(t);r.fill(!0,v[0],v[1]),s.fill(R.mean,v[0],v[1])}})),e[i]=s})),e}call_mean_shift(t=3){for(var e=new Array(this.rd.length).fill(!1),i=new Array(this.rd.length),n=0;n{var s=e.map(((t,e)=>!t)),o=[];s.forEach(((t,e)=>{t&&o.push(this.rd[e])}));for(var a=[0],l=0,h=0;h0&&(a.push(a[a.length-1]+l-1),l=0):l+=1;a.shift();for(var c=0;c=o.length||Math.abs(h-f)>=o.length)){var p=(f-h)*Math.exp(-.5*(f-h)**2/n**2)*Math.exp(-.5*(o[h]-o[f])**2*u[h]);d[h]+=p}var g=new Array;for(h=0;h=0&&g.push(h);g.push(d.length-1),g=g.concat(a).sort(((t,e)=>t-e)),g=Array.from(new Set(g));var m=0;for(h=0;ht+e))/b.length;o.fill(y,m,g[h]+1),m=g[h]+1}}for(h=0,f=0;h.01&&g.push(h+1);for(g.unshift(0),g.push(i.length),e=new Array(this.rd.length).fill(!1),h=1;h1){w[0]=g[h-2];var _=[g[h],g[h]];if(h3.483106931382794e-9*(x+k))continue;if(mb(C.mean,C.std,C.data.length,M.mean,M.std,M.data.length)>3.483106931382794e-9*(x+S))continue}if(!(gb(this.mean,C.mean,C.std,C.data.length)>.05)){var R=new pb(this.rd.slice(v[0],v[1]));e.fill(!0,v[0],v[1]),i.fill(R.mean,v[0],v[1])}}}}}})),i}cnv_calling(t=1e5){var e=(e=.25)*this.mean,i=this.mean-e,n=this.mean+e,r=this.meanShiftCaller(),s={},o=[];return Object.entries(r).forEach((([a,l])=>{for(var h=!1;!h;){h=!0;var c=new Array(1).fill(0);for(let t=0;t.01&&c.push(t+1);c.push(l.length);for(let t=0;t0&&(d=Math.abs(l[c[t]]-l[c[t-1]])),t{g.push(e.binScore)}));for(var m,b=new Array(l.length).fill(""),y=0,v=.05*t/2971e6;y_+1){var x=fb(this.mean,this.std,g,_,k,v);if(x){var k=x;b.fill("D",_,k)}}for(_=y;yn;)y+=1;(k=y)>_+1&&(x=fb(this.mean,this.std,g,_,k,v))&&(k=x,b.fill("A",_,k)),y==w&&(y+=1)}for(y=0;y_+1&&(db(this.mean,this.std,g,_,k)<1682935038707506e-26&&b.fill(["d"]*(k-_),_,k),y-=1),y+=1}(y=0)=b.length););if(y>_){var C=new pb(S.slice(_,y));S.fill(C.mean,_,y)}ya&&(s>0&&e.push({chr:i,start:o,end:a,value:r,bin:l,count:s}),r=0,o=n.start-n.start%this.binSize,a=o+this.binSize);const h=n.calls[9].info.DP;h&&(r+=Number.parseInt(h),s++)}s>0&&e.push({chr:i,start:o,end:a,value:r,bin:l,count:s})}return e}async computeReadDepth(){const t=Object.keys(this.allVariants);var e={};for(let n of t){const t=this.allVariants[n];var i;if(0!==t.length)for(let r of t){i=Math.max(Math.floor(r.start/this.rowBinSize),0),e[n]||(e[n]=[]),e[n][i]||(e[n][i]={chr:n,start:i*this.rowBinSize,end:(i+1)*this.rowBinSize,value:0,sum_score:0,count:0});const t=r.calls[9].info.DP;t&&(e[n][i].sum_score+=Number.parseInt(t),e[n][i].count++)}}var n={};for(let i of t){n[i]||(n[i]=[]);for(let t=0;t{e.forEach(((e,i)=>{e.partition_level=parseInt(s[t][i]),e.partition_call=parseInt(o[0][t][i])}))})),[this.formatDataStructure(t,"binScore",i),this.formatDataStructure(t,"partition_level",i),this.formatDataStructure(t,"partition_call",i),o[1]]}formatDataStructure(t,e,i=1){const n=[];for(const[r,s]of Object.entries(t))s.forEach((t=>{var r={...t};1!=i&&(r.value=t[e]/i*2),n.push(r)}));return n}async computeBAF_v2(){const t=Object.keys(this.allVariants),e={},i=[],n=[];for(let o of t){const t=this.allVariants[o];if(0===t.length)continue;var r;for(let a of t){if(r=Math.max(Math.floor(a.start/this.binSize),0),e[o]||(e[o]=[]),!e[o][r]){if(r>0){let t=r-1;if(e[o][t]){const r=this.get_max_min_score(e[o][t]);if(.5!=r.value){let t=Object.assign({},r);t.value=-2*(1-r.value),n.push(t)}r.value=-2*r.value,e[o][t]=r,i.push(e[o][t])}}e[o][r]={chr:o,start:r*this.binSize,end:(r+1)*this.binSize,value:0,count:0,likelihood_score:[],min_score:0}}const t=a.calls[9];let l=t.genotype,h=t.info.AD.split(","),c=h[0],u=h[1];if(0==l[0]&&1==l[1]||1==l[0]&&0==l[1]){if(0==e[o][r].likelihood_score.length)e[o][r].likelihood_score=Gm(0,1,100).map(((t,e)=>vb(c,u,t)));else{var s=0;e[o][r].likelihood_score=Gm(0,1,100).map(((t,i)=>{var n=e[o][r].likelihood_score[i]*vb(c,u,t);return s+=n,n})),e[o][r].likelihood_score=Gm(0,1,100).map(((t,i)=>e[o][r].likelihood_score[i]/s))}e[o][r].count++}}const a=this.get_max_min_score(e[o][r]);if(.5!=a.value){let t=Object.assign({},a);t.value=-2*(1-a.value),n.push(t)}a.value=-2*a.value,e[o][r]=a,i.push(e[o][r])}return[i,n]}format_BAF_likelihood(t){const e=[];for(const[i,n]of Object.entries(t))n.forEach((t=>{var i={...t};.5!=t.value&&(i.value=1-t.value,e.push(i))}));return e}get_max_min_score(t){if(t.likelihood_score.length>0){const e=Math.max(...t.likelihood_score),i=t.likelihood_score.indexOf(e);t.value=Math.max(i/100,1-i/100),t.min_score=Math.min(i/100,1-i/100)}else t.score=0;return t}async getAllbins(){const t=await this.computeDepthFeatures();return new Zm(t).fit_data(),t}async read_rd_baf(t="ReadDepth"){const e=Object.keys(this.allVariants);var i={};for(let t of e){const e=this.allVariants[t];var n;if(0!==e.length)for(let r of e){n=Math.max(Math.floor(r.start/this.rowBinSize),0),i[t]||(i[t]=[]),i[t][n]||(i[t][n]={chr:t,start:n*this.rowBinSize,end:(n+1)*this.rowBinSize,dp_sum_score:0,dp_count:0,hets_count:0,hets:[]});const e=r.calls[9],s=e.info.DP;s&&(i[t][n].dp_sum_score+=Number.parseInt(s),i[t][n].dp_count++);let o=e.info.AD.split(","),a=e.genotype;if(0==a[0]&&1==a[1]||1==a[0]&&0==a[1]){i[t][n].hets_count++;let e=parseInt(o[0]),r=parseInt(o[1]);i[t][n].hets.push({ref:e,alt:r})}}}var r,s=this.adjust_bin_size(i);if("ReadDepth"==t){r=this.readDepthMeanshift(s);var o=this.formatDataStructure_BAF(s,"max_likelihood")}else if("2D"==t){let t=new hb(s,this.binSize),e=await t.call_2d();r=[e.binScore,[],e.segment_score],o=t.formatDataStructure_BAF("max_likelihood")}return[r,o]}formatDataStructure_BAF(t,e,i=2){const n=[],r=[];for(const[i,s]of Object.entries(t))s.forEach((t=>{delete t.likelihood_score;var i={...t},s={...t};let o=t[e];.5!=o&&(s.value=-2*(1-o),r.push(s)),i.value=-2*o,n.push(i)}));return[n,r]}adjust_bin_size(t){const e=Object.keys(this.allVariants);var i={};for(let s of e){i[s]||(i[s]=[]);for(let e=0;e{if(0==i[s][e].likelihood_score.length)i[s][e].likelihood_score=Gm(0,1,100).map(((e,i)=>vb(t.ref,t.alt,e)));else{var r=0;i[s][e].likelihood_score=Gm(0,1,100).map(((n,o)=>{var a=i[s][e].likelihood_score[o]*vb(t.ref,t.alt,n);return r+=a,a})),i[s][e].likelihood_score=Gm(0,1,100).map(((t,n)=>i[s][e].likelihood_score[n]/r))}}))}const a=this.get_max_min_score(i[s][e]);i[s][e].max_likelihood=a.value}}return i}}function vb(t,e,i,n=!0){return i**t*(1-i)**e+i**e*(1-i)**t}class wb extends ch{constructor(t,e){super(t,e),this.featureType="numeric",this.paintAxis=$u,t.max||(this.defaultScale=!0,this.autoscale=!1),this.height=void 0!==t.height?t.height:250}async init(t){this.type="cnvpytor",this.graphType=t.graphType||"points",this.bin_size=t.bin_size||1e5,this.signal_name=t.signal_name||"rd_snp",this.cnv_caller=t.cnv_caller||"2D",this.colors=t.colors||["gray","black","green","blue"],super.init(t)}get supportsWholeGenome(){return!0}get_signals(){let t=[];return"rd_snp"==this.signal_name?t=["RD_Raw","RD_Raw_gc_coor",this.cnv_caller,"BAF1","BAF2"]:"rd"==this.signal_name?t=["RD_Raw","RD_Raw_gc_coor",this.cnv_caller]:"snp"==this.signal_name?t=["BAF1","BAF2"]:"cnh"==this.signal_name&&(t=[this.cnv_caller]),t}get_signal_colors(){return[{singal_name:"RD_Raw",color:this.colors[0]},{singal_name:"RD_Raw_gc_coor",color:this.colors[1]},{singal_name:"ReadDepth",color:this.colors[2]},{singal_name:"2D",color:this.colors[2]},{singal_name:"BAF1",color:this.colors[3]},{singal_name:"BAF2",color:this.colors[3]}]}async postInit(){if("vcf"==this.config.format){this.featureSource=$c(this.config,this.browser.genome),this.header=await this.getHeader();var t=this.featureSource.reader.features.reduce((function(t,e){return t[e.chr]=t[e.chr]||[],t[e.chr].push(e),t}),Object.create(null));const e=new yb(t,this.bin_size);let i,n,r;this.wigFeatures_obj={},this.wigFeatures_obj[this.bin_size]={},"2D"==this.config.cnv_caller?(r=await e.read_rd_baf("2D"),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size]["2D"]=i[2],this.available_callers=["2D"]):(r=await e.read_rd_baf(),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size].ReadDepth=i[2],this.available_callers=["ReadDepth"]),this.wigFeatures_obj[this.bin_size].RD_Raw=i[0],this.wigFeatures_obj[this.bin_size].RD_Raw_gc_coor=i[1],this.wigFeatures_obj[this.bin_size].BAF1=n[0],this.wigFeatures_obj[this.bin_size].BAF2=n[1],this.available_bins=[this.bin_size],this.set_available_callers()}else this.cnvpytor_obj=new $m(this.config.url,this.bin_size),this.wigFeatures_obj=await this.cnvpytor_obj.get_rd_signal(this.bin_size),this.available_bins=this.cnvpytor_obj.available_bins,this.available_callers=this.cnvpytor_obj.callers,this.set_available_callers();this.tracks=[];const e=[];this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(let t in this.wigFeatures_obj)for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:"wig",isMergedTrack:!0};t.features=n,t.name=i,t.color=this.signal_colors.filter((t=>t.singal_name===i)).map((t=>t.color));const r=await this.browser.createTrack(t);r?(r.autoscale=!1,this.tracks.push(r)):console.warn("Could not create track "+t),"function"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return Promise.all(e)}set_available_callers(){this.available_callers.includes(this.cnv_caller)||(this.available_callers.length>0?this.cnv_caller=this.available_callers[0]:this.cnv_caller=null)}async getHeader(){if(!this.header){if("function"==typeof this.featureSource.getHeader){const t=await this.featureSource.getHeader();t&&(this.callSets=t.callSets||[]),this.header=t}this.sampleNames=this.callSets?this.callSets.map((t=>t.name)):[]}return this.header}get height(){return this._height}set height(t){if(this._height=t,this.tracks)for(let e of this.tracks)e.height=t,e.config.height=t}menuItemList(){let t=[];void 0!==this.flipAxis&&t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),t=t.concat(Ui.numericDataMenuItems(this.trackView)),t.push("
"),t.push("Bin Sizes");for(let e of this.available_bins){const i=zi(e,e===this.bin_size);t.push({object:fe(i),click:async()=>{this.bin_size=e,await this.recreate_tracks(e),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}t.push("
"),t.push("Signal Type");let e={rd_snp:"RD and BAF Likelihood",rd:"RD Signal",snp:"BAF Likelihood"};for(let i in e){const n=zi(e[i],i===this.signal_name);t.push({object:fe(n),click:async()=>{this.signal_name=i,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}t.push("
"),t.push("CNV caller");for(let e of this.available_callers){const i=zi(e,e===this.cnv_caller);t.push({object:fe(i),click:async()=>{this.cnv_caller=e,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}return t}async recreate_tracks(t){this.tracks=[];const e=[];t in this.wigFeatures_obj||(this.wigFeatures_obj={...this.wigFeatures_obj,...await this.cnvpytor_obj.get_rd_signal(t)}),this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:"wig",isMergedTrack:!0};t.features=n,t.name=i,t.color=this.signal_colors.filter((t=>t.singal_name===i)).map((t=>t.color));const r=await this.browser.createTrack(t);r?(r.autoscale=!1,this.tracks.push(r)):console.warn("Could not create track "+t),"function"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return Promise.all(e)}async getFeatures(t,e,i,n){if(this.tracks){const r=this.tracks.map((r=>r.getFeatures(t,e,i,n)));return Promise.all(r)}}getScaleFactor(t,e,i,n){return n?i/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):i/(e-t)}computeYPixelValue(t,e){return(this.flipAxis?t-this.dataRange.min:this.dataRange.max-t)*e}computeYPixelValueInLogScale(t,e){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),t=Math.log10(t+1),(this.flipAxis?t-n:i-t)*e)}draw(t){const e=t.features;if(!e)return;if(this.defaultScale&&("rd_snp"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||-2,max:this.config.max||this.dataRange.max||6}:"rd"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||0,max:this.config.max||this.dataRange.max||6}:"snp"==this.signal_name&&(this.dataRange={min:this.config.min||this.dataRange.min||-2,max:this.config.max||this.dataRange.max||0})),this.autoscale&&(this.dataRange=function(t,e){let i=0,n=-Number.MAX_VALUE;for(let t of e)for(let e of t)void 0===e.value||Number.isNaN(e.value)||(i=Math.min(i,e.value),n=Math.max(n,e.value));return{min:i,max:n}}(t.referenceFrame.chr,e)),this.tracks)for(let i=0,n=this.tracks.length;ithis.logScale?this.computeYPixelValueInLogScale(t,i):this.computeYPixelValue(t,i);if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let i=n(e.y),r={strokeStyle:e.color,strokeWidth:1};e.dotted?na.dashedLine(t.context,0,i,t.pixelWidth,i,5,r):na.strokeLine(t.context,0,i,t.pixelWidth,i,r)}}popupData(t,e){const i=e||t.viewport.cachedFeatures;if(i&&i.length===this.tracks.length){const e=[];for(let n=0;n0&&e.push("
"),e.push(`
${this.tracks[n].name}
`);const r=this.tracks[n].popupData(t,i[n]);e.push(...r)}return e}}}const _b=new Map([["ideogram",(t,e)=>new zf(t,e)],["sequence",(t,e)=>new Xa(t,e)],["feature",(t,e)=>new Nd(t,e)],["seg",(t,e)=>new gf(t,e)],["mut",(t,e)=>new gf(t,e)],["maf",(t,e)=>new gf(t,e)],["wig",(t,e)=>new uf(t,e)],["merged",(t,e)=>new bf(t,e)],["alignment",(t,e)=>new jd(t,e)],["interaction",(t,e)=>new vf(t,e)],["interact",(t,e)=>new vf(t,e)],["variant",(t,e)=>new If(t,e)],["eqtl",(t,e)=>new Mf(t,e)],["gwas",(t,e)=>new Bf(t,e)],["arc",(t,e)=>new Of(t,e)],["gcnv",(t,e)=>new Nf(t,e)],["junction",(t,e)=>new jf(t,e)],["blat",(t,e)=>new Ud(t,e)],["cnvpytor",(t,e)=>new wb(t,e)]]);var xb=function(t,e){_b.set(t,e)};class kb{constructor(t,e){const i=(new DOMParser).parseFromString(t,"text/xml");this.processRootNode(i,e);const n=i.getElementsByTagName("Resource"),r=i.getElementsByTagName("Track"),s=r&&r.length>0,o=[];this.tracks=o;const a=new Map;Array.from(n).forEach((function(t,e){var i={url:t.getAttribute("path"),indexURL:t.getAttribute("index"),order:e};a.set(i.url,i),s||o.push(i)})),s&&Array.from(r).forEach((function(t){const e=t.getElementsByTagName("Track");if(e&&e.length>0){const i={type:"merged",tracks:[]};Sb(t,i),o.push(i),Array.from(e).forEach((function(t){t.processed=!0;const e=t.getAttribute("id"),n=a.get(e);n&&(i.tracks.push(n),Sb(t,n),n.autoscale=!1,i.height=n.height)}))}else if(!t.processed){const e=t.getAttribute("id"),i=a.get(e);i&&(o.push(i),Sb(t,i))}}))}processRootNode(t,e){const i=t.getElementsByTagName("Session");!i||i.length;const n=i.item(0),r=n.getAttribute("genome"),s=n.getAttribute("locus"),o=n.getAttribute("ucscID");e&&e.hasOwnProperty(r)?this.genome=r:(this.reference={fastaURL:r},o&&(this.reference.id=o)),s&&(this.locus=s)}}function Sb(t,e){e.name=t.getAttribute("name");const i=t.getAttribute("color");i&&(e.color="rgb("+i+")");const n=t.getAttribute("altColor");i&&(e.altColor="rgb("+n+")");const r=t.getAttribute("height");r&&(e.height=parseInt(r));const s=t.getAttribute("autoScale");s&&(e.autoscale="true"===s);const o=t.getAttribute("autoscaleGroup");o&&(e.autoscaleGroup=o);const a=t.getAttribute("windowFunction");a&&(e.windowFunction=a);const l=t.getAttribute("visibilityWindow")||t.getAttribute("featureVisibilityWindow");l&&(e.visibilityWindow=l);const h=t.getAttribute("indexed");h&&(e.indexed="true"===h);const c=t.getAttribute("normalize");c&&(e.normalize="true"===c);const u=t.getElementsByTagName("DataRange");if(u.length>0){const t=u.item(0);e.min=Number(t.getAttribute("minimum")),e.max=Number(t.getAttribute("maximum")),e.logScale="LOG"===t.getAttribute("type")}}const Cb=qi;class Ab{constructor(){this.attributes={},this.plinkLoaded=!1}async loadPlinkFile(t,e){e||(e={});var i=la(e);const n=await zo.loadString(t,i);var r=Cb(n);for(let t of r){var s=t.split(" ");this.attributes[s[1]]={familyId:s[0],fatherId:s[2],motherId:s[3],sex:s[4],phenotype:s[5]}}return this.plinkLoaded=!0,this}getAttributes(t){return this.attributes[t]}getAttributeNames(){return this.hasAttributes()?Object.keys(this.attributes[Object.keys(this.attributes)[0]]):[]}hasAttributes(){return Object.keys(this.attributes).length>0}}class Tb{constructor(t,e){this.geneColors={},this.gene=null,this.snp=null,this.genesCount=0,t&&(this.gene=t.toUpperCase(),this.geneColors[this.gene]=Ib[this.genesCount++]),e&&(this.snp=e.toUpperCase())}addGene(t){this.geneColors[t.toUpperCase()]||(this.geneColors[t.toUpperCase()]=Ib[this.genesCount++])}colorForGene(t){return this.geneColors[t.toUpperCase()]}}var Ib=[];Ib.push("rgb(228,26,28)"),Ib.push("rgb(55,126,184)"),Ib.push("rgb(77,175,74)"),Ib.push("rgb(166,86,40)"),Ib.push("rgb(152,78,163)"),Ib.push("rgb(255,127,0)"),Ib.push("rgb(247,129,191)"),Ib.push("rgb(153,153,153)"),Ib.push("rgb(255,255,51)"),Ib.push("rgb(102, 194, 165"),Ib.push("rgb(252, 141, 98"),Ib.push("rgb(141, 160, 203"),Ib.push("rgb(231, 138, 195"),Ib.push("rgb(166, 216, 84"),Ib.push("rgb(255, 217, 47"),Ib.push("rgb(229, 196, 148"),Ib.push("rgb(179, 179, 179"),Ib.push("rgb( 141, 211, 199"),Ib.push("rgb(255, 255, 179"),Ib.push("rgb(190, 186, 218"),Ib.push("rgb(251, 128, 114"),Ib.push("rgb(128, 177, 211"),Ib.push("rgb(253, 180, 98"),Ib.push("rgb(179, 222, 105"),Ib.push("rgb(252, 205, 229"),Ib.push("rgb(217, 217, 217"),Ib.push("rgb(188, 128, 189"),Ib.push("rgb(204, 235, 197"),Ib.push("rgb(255, 237, 111");class Eb{constructor(t,e,i,n,r){this.genome=t,this.chr=e,this.start=i,this.end=n,this.bpPerPixel=r,this.id=_e.guid()}extend(t){const e=Math.min(t.start,this.start),i=Math.max(t.end,this.end),n=(i-e)/(this.end-this.start);this.start=e,this.end=i,this.bpPerPixel*=n}calculateEnd(t){return this.start+this.bpPerPixel*t}calculateBPP(t,e){return(t-this.start)/e}set(t){this.chr=t.chr,this.start=t.start,this.bpPerPixel=t.bpPerPixel}toPixels(t){return t/this.bpPerPixel}toBP(t){return this.bpPerPixel*t}shiftPixels(t,e,i){const n=this.start,r=t*this.bpPerPixel;return this.start+=r,i&&this.clampStart(e),this.end=this.start+e*this.bpPerPixel,n!==this.start}clampStart(t){const e=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(e,this.start),t){const{bpLength:e}=this.genome.getChromosome(this.chr),i=e-t*this.bpPerPixel;this.start>i&&(this.start=i)}}async zoomWithScaleFactor(t,e,i,n){const r=void 0===n?this.start+this.toBP(i/2):n,{start:s,bpPerPixel:o}=this.start,{bpLength:a}=this.getChromosome(),l=e<1?t.minimumBases()/i:a/i;this.bpPerPixel=e<1?Math.max(this.bpPerPixel*e,l):Math.min(this.bpPerPixel*e,l);const h=this.bpPerPixel*i;this.start=r-.5*h,this.clampStart(i),this.end=this.start+h,(s!==this.start||o!==this.bpPerPixel)&&await t.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabelBPLengthOnly(t){const e=" ",i=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*t);return`${e}${this.chr}${e}${da(n-i)}${e}`}getMultiLocusLabelLocusOnly(t){const e=" ",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(t);return`${e}${i}:${n}-${r}${e}`}getMultiLocusLabel(t){const e=" ",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(t),s=Math.floor(this.start)+1;return`${e}${i}:${n}-${r}${e}${e}(${da(Math.round(this.start+this.bpPerPixel*t)-s)})${e}`}getPresentationLocusComponents(t){if("all"===this.chr)return{chr:this.chr};{const e=$i(Math.floor(this.start)+1),i=$i(Math.round(this.start+this.bpPerPixel*t));return{chr:this.chr,start:e,end:i}}}getLocusString(){if("all"===this.chr)return"all";{const t=$i(Math.floor(this.start)+1),e=$i(Math.round(this.end));return`${this.chr}:${t}-${e}`}}description(t){console.log(` ${t||""} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${$i(Math.round(this.start))} end ${$i(Math.round(this.end))} `)}}const Mb={timeout:5e3,type:"plain",url:"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$",coords:0,chromosomeField:"chromosome",startField:"start",endField:"end",geneField:"gene",snpField:"snp"};class Rb{constructor(t){this.browser=t}navbarDidResize(t){this.updateNavbar(this.createResponsiveClassSchedule(t))}updateNavbar(t){this.browser.$toggle_button_container.removeClass(),this.browser.$toggle_button_container.addClass(t.$toggle_button_container),fe(this.browser.zoomWidget.zoomContainer).removeClass(),fe(this.browser.zoomWidget.zoomContainer).addClass(t.zoomContainer)}createResponsiveClassSchedule(t){let e={};const i=this.browser.isMultiLocusWholeGenomeView()||this.browser.referenceFrameList&&ul.isWholeGenomeView(this.browser.referenceFrameList[0].chr);return i?this.browser.windowSizePanel.hide():this.browser.windowSizePanel.show(),t>990?(e.$toggle_button_container="igv-navbar-toggle-button-container",e.zoomContainer="igv-zoom-widget"):t>860?(e.$toggle_button_container="igv-navbar-toggle-button-container",e.zoomContainer="igv-zoom-widget-900"):t>540?(e.$toggle_button_container="igv-navbar-toggle-button-container-750",e.zoomContainer="igv-zoom-widget-900"):(e.$toggle_button_container="igv-navbar-toggle-button-container-750",e.zoomContainer="igv-zoom-widget-900",this.browser.windowSizePanel.hide()),i&&(e.zoomContainer="igv-zoom-widget-hidden"),e}}const Lb=function(t,e){this.container=_e.div({class:"igv-chromosome-select-widget-container"}),e.appendChild(this.container),this.select=document.createElement("select"),this.select.setAttribute("name","chromosome-select-widget"),this.container.appendChild(this.select),this.select.addEventListener("change",(()=>{this.select.blur(),""!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes};Lb.prototype.show=function(){this.container.style.display="flex"},Lb.prototype.hide=function(){this.container.style.display="none"},Lb.prototype.update=function(t){const e=this.showAllChromosomes?t.chromosomeNames.slice():t.wgChromosomeNames.slice();t.showWholeGenomeView()&&(e.unshift("all"),e.unshift("")),this.select.innerHTML="";for(let t of e){const e=document.createElement("option");e.setAttribute("value",t),e.innerText=t,this.select.appendChild(e)}};class Bb{constructor(t,e){this.container=_e.div({class:"igv-windowsize-panel-container"}),t.appendChild(this.container),e.on("locuschange",(t=>{this.updatePanel(t)})),this.browser=e}show(){this.container.style.display="block"}hide(){this.container.style.display="none"}updatePanel(t){const e=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===t.length?da(Math.round(e*t[0].bpPerPixel)):""}}class Nb{constructor(t,e){this.browser=e,this.columnContainer=t,this.horizontalGuide=_e.div({class:"igv-cursor-guide-horizontal"}),t.appendChild(this.horizontalGuide),this.verticalGuide=_e.div({class:"igv-cursor-guide-vertical"}),t.appendChild(this.verticalGuide),this.addMouseHandler(e),this.setVisibility(e.config.showCursorGuide)}addMouseHandler(t){this.boundMouseMoveHandler=function(e){const{x:i,y:n}=_e.translateMouseCoordinates(e,this.columnContainer);this.horizontalGuide.style.top=`${n}px`;const r=function(t,e){for(;t.parentElement;){if(t.parentElement.classList.contains("igv-viewport"))return t.parentElement;t=t.parentElement}}(document.elementFromPoint(e.clientX,e.clientY));if(r&&t.getRulerTrackView()){this.verticalGuide.style.left=`${i}px`;const n=t.root.querySelectorAll(".igv-column");let s;const o=r.parentElement;for(let t=0;t{t.cursorGuideVisible=!t.cursorGuideVisible,t.setCursorGuideVisibility(t.cursorGuideVisible),this.setButtonState(t.cursorGuideVisible)})),this.setButtonState(t.cursorGuideVisible),t.config.showCursorTrackingGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setButtonState(this.browser.cursorGuideVisible)}hide(){this.button.style.display="none"}}class Ob{constructor(t,e){this.browser=t,this.button=_e.div({class:"igv-navbar-button"}),e.appendChild(this.button),this.button.textContent="center line",this.button.addEventListener("click",(()=>{t.isCenterLineVisible=!t.isCenterLineVisible,t.setCenterLineVisibility(t.isCenterLineVisible),this.setButtonState(t.isCenterLineVisible)})),this.setButtonState(t.isCenterLineVisible),t.config.showCenterGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.isVisible=!0,this.button.style.display="block",this.setButtonState(this.browser.isCenterLineVisible)}hide(){this.isVisible=!1,this.button.style.display="none"}}class Db{constructor(t,e){this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="track labels",this.button.addEventListener("click",(()=>{e.trackLabelsVisible=!e.trackLabelsVisible,this.setState(e.trackLabelsVisible),e.setTrackLabelVisibility(e.trackLabelsVisible)})),this.browser=e,this.setVisibility(e.config.showTrackLabelButton),this.setState(e.trackLabelsVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.trackLabelsVisible)}hide(){this.button.style.display="none"}}class Pb{constructor(t,e){this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.innerText="Sample Names",this.setState(e.showSampleNames),this.setVisibility(e.showSampleNameButton),this.button.addEventListener("click",(()=>{e.showSampleNames=!e.showSampleNames,this.setState(e.showSampleNames);for(let{sampleNameViewport:t}of e.trackViews)!1===e.showSampleNames?t.hide():t.show();e.layoutChange()}))}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}hide(){this.button.style.display="none"}show(){this.button.style.display="block"}}let zb=23,Ub=0;const Vb=function(t,e){this.browser=t,this.zoomContainer=_e.div({class:"igv-zoom-widget"}),e.appendChild(this.zoomContainer),this.zoomOutButton=_e.div(),this.zoomContainer.appendChild(this.zoomOutButton),this.zoomOutButton.appendChild(_i.createIcon("minus-circle")),this.zoomOutButton.addEventListener("click",(()=>{t.zoomOut()}));const i=_e.div();this.zoomContainer.appendChild(i),this.slider=document.createElement("input"),this.slider.type="range",this.slider.min="0",this.slider.max=`${zb}`,i.appendChild(this.slider),this.slider.addEventListener("change",(e=>{e.preventDefault(),e.stopPropagation();const i=t.referenceFrameList[0],{bpLength:n}=i.genome.getChromosome(i.chr),{end:r,start:s}=i,o=r-s,a=n/Math.pow(2,e.target.valueAsNumber);t.zoomWithScaleFactor(a/o)})),this.zoomInButton=_e.div(),this.zoomContainer.appendChild(this.zoomInButton),this.zoomInButton.appendChild(_i.createIcon("plus-circle")),this.zoomInButton.addEventListener("click",(()=>{t.zoomIn()})),t.on("locuschange",(t=>{this.browser.isMultiLocusMode()?this.disable():(this.enable(),this.update(t))}))};Vb.prototype.update=function(t){const e=t[0],{bpLength:i}=e.genome.getChromosome(e.chr),{start:n,end:r}=e;zb=Math.ceil(Math.log2(i/this.browser.minimumBases())),this.slider.max=`${zb}`;const s=i/(r-n);Ub=Math.log2(s),this.slider.value=`${Math.round(Ub)}`},Vb.prototype.enable=function(){this.slider.disabled=!1},Vb.prototype.disable=function(){this.slider.disabled=!0},Vb.prototype.hide=function(){this.zoomContainer.style.display="none"},Vb.prototype.show=function(){this.zoomContainer.style.display="block"},Vb.prototype.hideSlider=function(){this.slider.style.display="none"},Vb.prototype.showSlider=function(){this.slider.style.display="block"};const Hb=function(t,e){const i=_e.div({class:"igv-navbar-button"});t.append(i),i.textContent="Save SVG",i.addEventListener("click",(()=>e.saveSVGtoFile({})))};class jb{constructor(t,e,i){this.browser=t,this.referenceFrame=e,this.column=i,this.container=_e.div({class:"igv-center-line"}),i.appendChild(this.container),t.isCenterLineVisible?this.show():this.hide()}repaint(){if(this.referenceFrame)if(1/this.referenceFrame.bpPerPixel>1){const t=Math.floor(this.referenceFrame.toPixels(1));this.container.style.width=`${t}px`,this.container.classList.remove("igv-center-line-thin"),this.container.classList.add("igv-center-line-wide")}else this.container.style.width="1px",this.container.classList.remove("igv-center-line-wide"),this.container.classList.add("igv-center-line-thin")}show(){this.isVisible=!0,this.container.style.display="block",this.repaint()}hide(){this.isVisible=!1,this.container.style.display="none"}resize(){this.repaint()}}const $b=$i;class qb{constructor(t){this.browser=t,this.height=40,this.name="",this.id="ruler",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type="ruler"}async getFeatures(t,e,i){return[]}computePixelHeight(t){return this.height}draw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n,bpPerPixel:r,bpStart:s}){ul.isWholeGenomeView(e.chr)?this.drawWholeGenome({context:t,pixelWidth:i,pixelHeight:n,bpPerPixel:r}):this.doDraw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n,bpStart:s})}drawWholeGenome({context:t,pixelWidth:e,pixelHeight:i,bpPerPixel:n}){t.save(),na.fillRect(t,0,0,e,i,{fillStyle:"white"});for(let e of this.browser.genome.wgChromosomeNames){let r=this.browser.genome.getCumulativeOffset(e),s=this.browser.genome.getChromosome(e).bpLength,o=Math.round(r/n),a=Math.round(s/n);this.renderChromosomeRect(t,o,0,a,i,e)}t.restore()}doDraw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n,bpStart:r}){t.clearRect(0,0,i,n);const s=function(t,e){if(t<10)return new Wb(1,"bp",1);const i=Math.floor(Math.log10(t));let n="bp",r=1;i>9?(n="gb",r=1e9):i>6?(n="mb",r=1e6):i>3&&(n="kb",r=1e3);const s=t/Math.pow(10,i-1),o=Math.pow(10,i-1),a=Math.pow(10,i)/2;return new Wb(s<75&&!0!==e?o:a,n,r)}(Math.floor(e.toBP(i)),t.isSVG);let o=Math.floor(r/s.majorTick)-1;const{tickDelta:a,labelLength:l}=function(t,e,i,n,r){const s=l(e,a(1+n,r),i)-l(e,a(n,r),i),o=`${$i(Math.floor(a(n,r)/r.unitMultiplier))} ${r.majorUnit}`;return{tickDelta:s,labelLength:Math.floor(t.measureText(o).width)};function a(t,e){return Math.floor(t*e.majorTick)}function l(t,e,i){return Math.round(t.toPixels(e-1-i+.5))}}(t,e,r,o,s);let h,c;this.browser.referenceFrameList.indexOf(e);let u=a;const d=.25*l;do{c=Math.floor(o*s.majorTick);const i=`${$i(Math.floor(c/s.unitMultiplier))} ${s.majorUnit}`;h=Math.round(e.toPixels(c-1-r+.5));const n=Math.round(h-t.measureText(i).width/2);n>0&&d+l<=u&&(na.fillText(t,i,n,this.height-8),u=0),h>0&&na.strokeLine(t,h,this.height-6,h,this.height-2),c=Math.floor((1+o)*s.majorTick);let f=h+(Math.round(e.toPixels(c-1-r+.5))-h)/2;f>0&&na.strokeLine(t,f,this.height-6,f,this.height-2),++o,u+=a}while(ht.measureText(o).width&&na.fillText(t,o,e+n/2,i+r/2,{fillStyle:xo.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Wb{constructor(t,e,i){this.majorTick=t,this.minorTick=t/10,this.majorUnit=e,this.unitMultiplier=i}description(t){console.log((t||"")+" tick "+$b(this.majorTick)+" label width "+$b(this.labelWidthBP)+" multiplier "+this.unitMultiplier)}}const Gb=function(t,e){this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="circular view",this.button.addEventListener("click",(()=>{e.circularViewVisible=!e.circularViewVisible})),this.browser=e,this.setVisibility(e.config.showCircularViewButton),this.setState(e.circularViewVisible)};Gb.prototype.setVisibility=function(t){!0===t?this.show():this.hide()},Gb.prototype.setState=function(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")},Gb.prototype.show=function(){this.button.style.display="block",this.setState(this.browser.circularViewVisible)},Gb.prototype.hide=function(){this.button.style.display="none"};const Zb=function(t,e,i){const n=_e.div({class:"igv-navbar-button"});t.append(n),n.textContent=i.label,n.addEventListener("click",(()=>i.callback(e)))};class Yb{constructor(t,e,i,n,r){this.browser=t,this.roiMenu=e,this.roiTable=i,this.top=n,this.roiSets=r||[],this.boundLocusChangeHandler=Qb.bind(this),t.on("locuschange",this.boundLocusChangeHandler)}async initialize(){this.roiSets.length>0&&(this.browser.showROITableButton=!0,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton));const t=this.roiSets.map((t=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})));t.length>0&&await Promise.all(t);const e=await this.getTableRecords();this.roiTable.renderTable(e)}async loadROI(t,e){const i=Array.isArray(t)?t:[t];for(let t of i)this.roiSets.push(new Gc(t,e));await this.initialize()}clearROIs(){this.roiTable.clearTable();const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();for(let t of this.roiSets)t.dispose();this.roiSets=[]}async getTableRecords(){const t=[];for(let e of this.roiSets){const i=e.isUserDefined?"":e.name||"",n=await e.getAllFeatures();for(let e of Object.keys(n))for(let r of n[e])t.push({setName:i,feature:r})}return t}presentTable(){this.roiTable.present()}async repaintTable(){const t=await this.getTableRecords();this.roiTable.renderTable(t)}dismissTable(){this.roiTable.dismiss()}async updateUserDefinedROISet(t){let e=await this.getUserDefinedROISet();void 0===e&&(e=this.initializeUserDefinedROISet()),e.addFeature(t),!1===this.browser.showROITableButton&&this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e});const i=await this.getTableRecords();this.roiTable.renderTable(i)}setROITableButtonVisibility(t){this.browser.showROITableButton=t,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton)}async renderAllROISets(){for(let t of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})}async renderROISet({browser:t,pixelTop:e,roiSet:i}){const n=t.columnContainer.querySelectorAll(".igv-column");for(let r=0;ra)&&t.remove()}const c=await i.getFeatures(s,o,a);if(c)for(let h of c){const c=Xb(s,h.start,h.end),{x:u,width:d}=Zc(Math.max(o,h.start),Math.min(a,h.end),o,l),f=n[r].querySelector(Kb(c));if(f)f.style.left=`${u}px`,f.style.width=`${d}px`;else{const s=this.createRegionElement(t.columnContainer,e,u,d,i,c,h.name);n[r].appendChild(s)}}}}createRegionElement(t,e,i,n,r,s,o){const a=_e.div({class:"igv-roi-region"});a.style.top=`${e}px`,a.style.left=`${i}px`,a.style.width=`${n}px`,a.style.backgroundColor=r.color,a.dataset.region=s;const l=_e.div();return a.appendChild(l),l.style.backgroundColor=r.headerColor,!0===r.isUserDefined?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation();const{x:i,y:n}=_e.translateMouseCoordinates(e,t);this.roiMenu.present(i,n,this,t,a)})):o?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation(),this.popover&&this.popover.dispose(),this.popover=new Oi(t,r.name),this.popover.presentContentWithEvent(e,o)})):l.style.pointerEvents="none",a}renderSVGContext(t,{deltaX:e,deltaY:i}){for(const n of document.querySelectorAll(".igv-roi-region")){const{x:r,y:s,width:o,height:a}=n.getBoundingClientRect();t.fillStyle=n.style.backgroundColor,t.fillRect(r+e,s+i,o,a);const l=n.querySelector("div"),{x:h,y:c,width:u,height:d}=l.getBoundingClientRect();t.fillStyle=l.style.backgroundColor,t.fillRect(h+e,c+i,u,d)}}async getUserDefinedROISet(){return this.roiSets.find((t=>!0===t.isUserDefined))}initializeUserDefinedROISet(){const t=new Gc({isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(t),t}async deleteUserDefinedRegionWithKey(t,e){e.querySelectorAll(Kb(t)).forEach((t=>t.remove()));const i=await this.findUserDefinedRegionWithKey(t),n=await this.getUserDefinedROISet();n&&n.removeFeature(i),0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}async findUserDefinedRegionWithKey(t){const{chr:e,start:i,end:n}=Jb(t),r=await this.getUserDefinedROISet();if(r){const t=await r.getFeatures(e,i,n);for(let r of t)if(r.chr===e&&r.start>=i&&r.end<=n)return r}}toJSON(){return this.roiSets.map((t=>t.toJSON()))}dispose(){this.browser.off("locuschange",this.boundLocusChangeHandler);const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let t of this.roiSets)t.dispose();for(let t of Object.keys(this))this[t]=void 0}}function Qb(){this.renderAllROISets()}function Xb(t,e,i){return`${t}-${e}-${i}`}function Kb(t){return`[data-region="${t}"]`}function Jb(t){let[e,i,n]=t.split("-");return i=parseInt(i),n=parseInt(n),{chr:e,start:i,end:n,locus:`${e}:${i}-${n}`,bedRecord:`${e}\t${i}\t${n}`}}class ty extends Fd{constructor(t){super(Object.assign({width:"512px"},t))}tableRowDOM(t){const e=_e.div({class:"igv-roi-table-row"}),{setName:i,feature:n}=t;e.dataset.region=Xb(n.chr,n.start,n.end);let r=[n.chr,$i(n.start),$i(n.end),n.name||"",i];4===this.columnFormat.length&&(r=r.slice(0,4));for(let t=0;tt.remove())),t.length>0){const e=t.sort(((t,e)=>t.feature.chr.localeCompare(e.feature.chr)||t.feature.start-e.feature.start||t.feature.end-e.feature.end));for(let t of e){const e=this.tableRowDOM(t);this.tableRowContainer.appendChild(e)}}}dispose(){document.removeEventListener("click",this.boundGotoButtonHandler),this.browser.roiTableControl.buttonHandler(!1),super.dispose()}static getColumnFormatConfiguration(t){return!0===t?[{label:"Chr",width:"20%"},{label:"Start",width:"15%"},{label:"End",width:"15%"},{label:"Description",width:"30%"},{label:"ROI Set",width:"20%"}]:[{label:"Chr",width:"25%"},{label:"Start",width:"20%"},{label:"End",width:"20%"},{label:"Description",width:"35%"}]}static gotoButtonHandler(t){t.stopPropagation();const e=this.tableDOM.querySelectorAll(".igv-roi-table-row-selected"),i=[];for(let t of e){const{locus:e}=Jb(t.dataset.region);i.push(e)}for(let t of this.tableDOM.querySelectorAll(".igv-roi-table-row"))t.classList.remove("igv-roi-table-row-selected");this.setTableRowSelectionState(!1),i.length>0&&this.browser.search(i.join(" "))}}class ey{constructor(t,e){this.browser=t,this.container=_e.div({class:"igv-roi-menu-next-gen"}),e.appendChild(this.container);const i=_e.div();this.container.appendChild(i),ki.attachDialogCloseHandlerWithParent(i,(()=>this.container.style.display="none")),this.body=_e.div(),this.container.appendChild(this.body),this.container.style.display="none"}async present(t,e,i,n,r){iy(this.body);const s=await this.browser.roiManager.findUserDefinedRegionWithKey(r.dataset.region),o=_e.div();this.body.appendChild(o);const a="Description",l=s.name||a;o.innerText=l,o.setAttribute("title",l),a===l?o.classList.add("igv-roi-placeholder"):o.classList.remove("igv-roi-placeholder");const h=_e.div();this.body.appendChild(h),h.innerText="Set Description",h.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none";const e={label:"Description",value:s.name||"",callback:()=>{const t=this.browser.inputDialog.value||"";s.name=t.trim(),this.container.style.display="none",this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(e,t)}));const c=_e.div();this.body.appendChild(c),c.innerText="Delete Region",c.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(r.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex"}async __present(t,e,i,n,r){iy(this.container);const s=await this.browser.roiManager.findUserDefinedRegionWithKey(r.dataset.region);let o;o=_e.div({class:"igv-roi-menu-row-edit-description"}),this.container.appendChild(o),o.addEventListener("click",(t=>{t.stopPropagation()}));const a="description-input",l=document.createElement("label");o.appendChild(l),l.setAttribute("for",a),l.innerText="Description:";const h=document.createElement("input");o.appendChild(h),h.setAttribute("type","text"),h.setAttribute("name",a),h.setAttribute("placeholder",""),h.value=s.name||"",h.addEventListener("change",(async t=>{t.stopPropagation(),(await this.browser.roiManager.findUserDefinedRegionWithKey(r.dataset.region)).name=h.value,h.blur(),this.container.style.display="none",await this.browser.roiManager.repaintTable()})),o=_e.div({class:"igv-roi-menu-row"}),o.innerText="Delete region",this.container.appendChild(o),o.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(r.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex",n.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none"}))}dispose(){this.container.innerHTML=""}}function iy(t){for(;t.firstChild;)t.removeChild(t.firstChild)}class ny{constructor(t,e){this.name=t.name,this.featureSource=t.featureSource||$c(t,e),this.color=t.color||qc}async getFeatures(t,e,i){return this.featureSource.getFeatures({chr:t,start:e,end:i})}draw(t){const{context:e,bpPerPixel:i,bpStart:n,pixelTop:r,pixelHeight:s,pixelWidth:o,features:a}=t;if(!a)return;const l=n+o*i+1;for(let{start:t,end:o}of a){if(ol)break;const{x:a,width:h}=Zc(t,o,n,i);na.fillRect(e,a,r,h,s,{fillStyle:this.color})}}}class ry{constructor(t,e){this.browser=e,this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="ROI Table",this.button.addEventListener("click",(()=>{this.buttonHandler(!e.roiTableVisible)})),this.browser=e,this.setVisibility(e.showROITableButton),this.setState(e.roiTableVisible)}buttonHandler(t){this.browser.roiTableVisible=t,this.setState(this.browser.roiTableVisible),this.browser.setROITableVisibility(this.browser.roiTableVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.roiTableVisible)}hide(){this.button.style.display="none"}}class sy{constructor(t,e){this.config=t,this.guid=_e.guid(),this.namespace=".browser_"+this.guid,this.parent=e,this.root=_e.div({class:"igv-container"}),e.appendChild(this.root),this.alert=new sa(this.root),this.columnContainer=_e.div({class:"igv-column-container"}),this.root.appendChild(this.columnContainer),this.menuPopup=new sf(this.columnContainer),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:"rgb(0,0,150)",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},this.addMouseHandlers(),this.setControls(t)}initialize(t){t.gtex&&(Sd.gtexLoaded=!0),this.flanking=t.flanking,this.crossDomainProxy=t.crossDomainProxy,this.formats=t.formats,this.trackDefaults=t.trackDefaults,this.nucleotideColors=t.nucleotideColors||$a;for(let t of Object.keys(this.nucleotideColors))this.nucleotideColors[t.toLowerCase()]=this.nucleotideColors[t];this.trackLabelsVisible=t.showTrackLabels,this.roiTableVisible=t.showROITable,this.showROITableButton=t.showROITableButton,this.isCenterLineVisible=t.showCenterGuide,this.cursorGuideVisible=t.showCursorGuide,this.showSampleNames=t.showSampleNames,this.showSampleNameButton=t.showSampleNameButton,this.sampleNameViewportWidth=t.sampleNameViewportWidth||200,t.search&&(this.searchConfig={type:"json",url:t.search.url,coords:void 0===t.search.coords?1:t.search.coords,chromosomeField:t.search.chromosomeField||"chromosome",startField:t.search.startField||"start",endField:t.search.endField||"end",geneField:t.search.geneField||"gene",snpField:t.search.snpField||"snp",resultsField:t.search.resultsField})}setControls(t){const e=this.createStandardControls(t);e.insertBefore(fe(this.columnContainer)),this.$navigation=e,!1===t.showControls&&e.hide()}createStandardControls(t){this.navbarManager=new Rb(this);const e=fe("
",{class:"igv-navbar"});this.$navigation=e;const i=fe("
",{class:"igv-navbar-left-container"});e.append(i);const n=fe("
",{class:"igv-logo"});i.append(n);const r=fe('IGV; ');r.css("width","34px"),r.css("height","32px"),n.append(r),this.$current_genome=fe("
",{class:"igv-current-genome"}),i.append(this.$current_genome),this.$current_genome.text("");const s=fe("
",{class:"igv-navbar-genomic-location"});i.append(s),this.chromosomeSelectWidget=new Lb(this,s.get(0)),void 0===t.showChromosomeWidget&&(t.showChromosomeWidget=!0),!0===t.showChromosomeWidget?this.chromosomeSelectWidget.show():this.chromosomeSelectWidget.hide();const o=fe("
",{class:"igv-locus-size-group"});s.append(o);const a=fe("
",{class:"igv-search-container"});o.append(a),this.$searchInput=fe("",{class:"igv-search-input",type:"text",placeholder:"Locus Search"}),a.append(this.$searchInput),this.$searchInput.change((()=>this.doSearch(this.$searchInput.val())));const l=_e.div({class:"igv-search-icon-container"});a.append(fe(l)),l.appendChild(_i.createIcon("search")),l.addEventListener("click",(()=>this.doSearch(this.$searchInput.val()))),this.windowSizePanel=new Bb(o.get(0),this);const h=fe("
",{class:"igv-navbar-right-container"});e.append(h);const c=fe('
');if(h.append(c),this.$toggle_button_container=c,this.cursorGuide=new Nb(this.columnContainer,this),this.cursorGuideButton=new Fb(this,c.get(0)),this.centerLineButton=new Ob(this,c.get(0)),this.setTrackLabelVisibility(t.showTrackLabels),this.trackLabelControl=new Db(c.get(0),this),this.roiTableControl=new ry(c.get(0),this),this.sampleNameControl=new Pb(c.get(0),this),!0===t.showSVGButton&&(this.svgSaveControl=new Hb(c.get(0),this)),t.customButtons)for(let e of t.customButtons)new Zb(c.get(0),this,e);return this.zoomWidget=new Vb(this,h.get(0)),!1===t.showNavigation&&this.$navigation.hide(),this.inputDialog=new Mi(this.root),this.inputDialog.container.id=`igv-input-dialog-${_e.guid()}`,this.dataRangeDialog=new Hi(this,fe(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${_e.guid()}`,this.genericColorPicker=new Pi({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${_e.guid()}`,e}getSampleNameViewportWidth(){return!1===this.showSampleNames?0:this.sampleNameViewportWidth}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}addTrackToFactory(t,e){xb(t,e)}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let t of this.referenceFrameList)if("all"===t.chr.toLowerCase())return!0;return!1}currentLoci(){const t=t=>`${t.chr}:${t.start+1}-${t.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?"":1===this.referenceFrameList.length?t(this.referenceFrameList[0]):this.referenceFrameList.map((e=>t(e)))}toSVG(){const{y:t,width:e,height:i}=this.columnContainer.getBoundingClientRect(),n=new ll({width:e,height:8e3,backdropColor:"white",multiLocusGap:0,viewbox:{x:0,y:0,width:e,height:8e3}}),r={deltaX:0,deltaY:-t};for(let t of this.trackViews)t.renderSVGContext(n,r);return this.roiManager.renderSVGContext(n,r),n.setHeight(i),n.getSerializedSvg(!0)}renderSVG(t){const e=this.toSVG();return t.empty(),t.append(e),e}saveSVGtoFile(t){let e=this.toSVG();t.$container&&(t.$container.empty(),t.$container.append(e)),Qi(t.filename||"igvjs.svg",URL.createObjectURL(new Blob([e],{type:"application/octet-stream"})))}async loadSession(t){let e;return this.roiSets=[],e=t.url||t.file?await async function(t){const e=t.url||t.file;if(t.url&&(t.url.startsWith("blob:")||t.url.startsWith("data:"))){const e=sy.uncompressSession(t.url);return JSON.parse(e)}{let i=t.filename;if(i||(i=t.url?await ua(t.url):t.file.name),i.endsWith(".xml")){const t=ul.KNOWN_GENOMES,i=await zo.loadString(e);return new kb(i,t)}return i.endsWith(".json")?zo.loadJson(e):void 0}}(t):t,this.loadSessionObject(e)}async loadSessionObject(t){this.cleanHouseForSession(),this.showSampleNames=t.showSampleNames||!1,this.sampleNameControl.setState(!0===this.showSampleNames),t.sampleNameViewportWidth&&(this.sampleNameViewportWidth=t.sampleNameViewportWidth),pa(this.columnContainer,"igv-axis-column"),pa(this.columnContainer,"igv-sample-name-column"),pa(this.columnContainer,"igv-scrollbar-column"),pa(this.columnContainer,"igv-track-drag-column"),pa(this.columnContainer,"igv-gear-menu-column");const e=t.reference||t.genome;if(!e)return void console.warn("No genome or reference object specified");const i=await ul.expandReference(this.alert,e);await this.loadReference(i,t.locus),this.centerLineList=this.createCenterLineList(this.columnContainer);let n=0;if(!1!==t.showIdeogram){const t=new zf(this);t.id="ideogram";const e=new hf(this,this.columnContainer,t),{$viewport:i}=e.viewports[0];n=function(t){t="string"==typeof t?document.querySelector(t):t;const e=window.getComputedStyle(t),i=parseFloat(e.marginTop)+parseFloat(e.marginBottom),n=t.offsetHeight;return Math.ceil(i+n)}(i.get(0)),this.trackViews.push(e)}if(!1!==t.showRuler&&this.trackViews.push(new hf(this,this.columnContainer,new qb(this))),t.gtexSelections)for(let e of this.referenceFrameList)for(let i of Object.keys(t.gtexSelections)){const n=t.gtexSelections[i].gene,r=t.gtexSelections[i].snp;e.selection=new Tb(n,r)}this.roiManager&&this.roiManager.dispose();const r=new ey(this,this.columnContainer),s={browser:this,parent:this.columnContainer,headerTitle:"Regions of Interest",dismissHandler:()=>this.roiTableControl.buttonHandler(!1),gotoButtonHandler:ty.gotoButtonHandler};if(t.roi){const e=t.roi.map((t=>new Gc(t,this.genome))),i=e.filter((({name:t})=>void 0!==t&&t.length>0));s.columnFormat=ty.getColumnFormatConfiguration(i.length>0);const o=new ty(s);this.roiManager=new Yb(this,r,o,n,e)}else{s.columnFormat=ty.getColumnFormatConfiguration(!1);const t=new ty(s);this.roiManager=new Yb(this,r,t,n,void 0)}await this.roiManager.initialize();const o=i.tracks||[],a=t.tracks?o.concat(t.tracks):o;0===a.filter((t=>"sequence"===t.type&&!t.url&&!t.fastaURL)).length&&a.push({type:"sequence",order:qa});let l=1;for(let t of a)void 0===t.order&&(t.order=l++);await this.loadTrackList(a);for(let t of this.trackViews.filter((t=>"ruler"===t.track.type||"ideogram"===t.track.type)))t.updateViews();this.updateUIWithReferenceFrameList()}createCenterLineList(t){const e=t.querySelectorAll(".igv-center-line");for(let t=0;tt.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}updateNavbarDOMWithGenome(t){let e=t.id&&t.id.length<10?t.id:"";this.$current_genome.text(e),this.$current_genome.attr("title",t.id||""),this.chromosomeSelectWidget.update(t)}async loadGenome(t){const e=await ul.expandReference(this.alert,t);await this.loadReference(e,void 0);const i=e.tracks||[];return 0===i.filter((t=>"sequence"===t.type)).length&&i.push({type:"sequence",order:qa}),await this.loadTrackList(i),await this.updateViews(),this.genome}updateUIWithReferenceFrameList(){const t=this.referenceFrameList;this.updateLocusSearchWidget();const e=this.isMultiLocusWholeGenomeView()||ul.isWholeGenomeView(t[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),e),hy(this.trackViews,this.trackLabelsVisible),this.setCenterLineAndCenterLineButtonVisibility(!ul.isWholeGenomeView(t[0].chr))}setTrackLabelVisibility(t){hy(this.trackViews,t)}setROITableVisibility(t){!0===t?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(t){t?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(t){this.cursorGuide.customMouseHandler=t}setCenterLineVisibility(t){for(let e of this.centerLineList)!0===t?(e.show(),e.repaint()):e.hide()}setCenterLineAndCenterLineButtonVisibility(t){for(let e of this.centerLineList)t&&e.isVisible?e.show():e.container.style.display="none";t&&this.centerLineButton.isVisible?this.centerLineButton.show():this.centerLineButton.button.style.display="none"}async loadTrackList(t){const e=[];for(let i of t)e.push(this._loadTrack(i));const i=await Promise.all(e);return this.trackViews.filter((function(t){return t.track.autoscaleGroup})).length>0&&this.updateViews(),i}async loadTrack(t){const e=this._loadTrack(t);return t.autoscaleGroup&&(await e,this.updateViews()),e}async _loadTrack(t){ji(t)&&(t=JSON.parse(t));try{const e=await this.createTrack(t);if(void 0===e)return;void 0===e.order&&(e.order=this.trackViews.length);const i=new hf(this,this.columnContainer,e);if(this.trackViews.push(i),hy(this.trackViews,this.trackLabelsVisible),this.reorderTracks(),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),"function"==typeof e.postInit)try{i.startSpinner(),await e.postInit()}finally{i.stopSpinner()}return e.autoscaleGroup||(t.sync?await i.updateViews():i.updateViews()),"function"==typeof e.hasSamples&&e.hasSamples()&&!1!==this.config.showSampleNameButton&&this.sampleNameControl.show(),e}catch(e){const i={401:"Access unauthorized",403:"Access forbidden",404:"Not found"};console.error(e);let n=e.message||e.error||e.toString();i.hasOwnProperty(n)&&(n=i[n]),n+=": "+t.url,this.alert.present(new Error(n),void 0)}}async loadROI(t){await this.roiManager.loadROI(t,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const t=await this.roiManager.getUserDefinedROISet();if(void 0===t)return[];const e=await t.getAllFeatures(),i=[];for(let t of Object.values(e))i.push(...t);return i}return[]}getRulerTrackView(){const t=this.trackViews.filter((({track:t})=>"ruler"===t.id));return t.length>0?t[0]:void 0}async createTrack(t){let e=await async function(t){return"function"==typeof t?t():t}(t.url||t.fastaURL);if(ji(e)&&(e=e.trim()),e)if(t.format)t.format=t.format.toLowerCase();else if(t.fastaURL)t.format="fasta";else{let i=t.filename;i||(i=await ua(e));const n=ka(i);"tsv"===n?t.format=await Aa(t):n?t.format=n:"htsget"===t.sourceType&&await cc.inferFormat(t)}let i=t.type?t.type.toLowerCase():void 0;if(!i){if(i=Ca(t),"bedtype"===i){const e=$c(t,this.genome);t._featureSource=e;i=await e.trackType()||"annotation"}t.type=i}if(this.trackDefaults&&i){const e=this.trackDefaults[i];if(e)for(let i in e)e.hasOwnProperty(i)&&void 0===t[i]&&(t[i]=e[i])}const n=function(t,e,i){let n;switch(t){case"annotation":case"genes":case"fusionjuncspan":case"snp":n="feature";break;case"seg":case"maf":case"mut":n="seg";break;case"junctions":case"splicejunctions":n="junction";break;default:n=t}return _b.has(n)?_b.get(n)(e,i):void 0}(i,t,this);if(void 0!==n)return t.roi&&t.roi.length>0&&(n.roiSets=t.roi.map((t=>new ny(t,this.genome)))),n;this.alert.present(new Error(`Error creating track. Could not determine track type for file: ${t.url||t}`),void 0)}reorderTracks(){this.trackViews.sort((function(t,e){const i=t=>"ideogram"===t.track.id?1:"ruler"===t.track.id?2:3,n=i(t),r=i(e);return n===r?(t.track.order||0)-(e.track.order||0):n-r}));for(let{axis:t,viewports:e,sampleNameViewport:i,outerScroll:n,dragHandle:r,gearContainer:s}of this.trackViews){t.remove();for(let{$viewport:t}of e)t.detach();i.viewport.remove(),n.remove(),r.remove(),s.remove()}const t=this.columnContainer.querySelectorAll(".igv-column");for(let{axis:e,viewports:i,sampleNameViewport:n,outerScroll:r,dragHandle:s,gearContainer:o}of this.trackViews){this.columnContainer.querySelector(".igv-axis-column").appendChild(e);for(let e=0;et.track&&t.track.name)).map((t=>t.track.name))}removeTrackByName(t){const e=this.trackViews.slice();for(let i of e)t===i.track.name&&this.removeTrack(i.track)}removeTrack(t){for(let e of this.trackViews)if(t===e.track){this._removeTrack(e.track);break}}_removeTrack(t){t.disposed||(this.trackViews.splice(this.trackViews.indexOf(t.trackView),1),this.fireEvent("trackremoved",[t]),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),t.trackView&&t.trackView.dispose())}removeAllTracks(){const t=[];for(let e of this.trackViews)"ruler"!==e.track.id&&"ideogram"!==e.track.id?(this.fireEvent("trackremoved",[e.track]),e.dispose()):t.push(e);this.trackViews=t}findTracks(t,e){let i="function"==typeof t?e=>t(e.track):i=>e===i.track[t];return this.trackViews.filter(i).map((t=>t.track))}setTrackHeight(t){this.trackHeight=t,this.trackViews.forEach((function(e){e.setTrackHeight(t)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((t=>t.bpPerPixel<0))){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel=(e.end-e.start)/t}if(this.referenceFrameList){const t=this.isMultiLocusWholeGenomeView()||ul.isWholeGenomeView(this.referenceFrameList[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),t)}oy.call(this),await this.updateViews()}async updateViews(){const t=this.trackViews;this.updateLocusSearchWidget();for(let t of this.centerLineList)t.repaint();if(this.dragObject)for(let e of t)await e.updateViews();else{const r={},s=[];for(let i of t){const t=i.track.autoscaleGroup;if(t){var e=r[t];e||(e=[],r[t]=e),e.push(i)}else s.push(i)}if(Object.entries(r).length>0){const t=Object.keys(r);for(let e of t){const t=r[e],s=[];for(let e of t)s.push(e.getInViewFeatures());const o=await Promise.all(s);var i,n=[];for(let t of o)n=n.concat(t);i=ha(n);const a=[];for(let e of t)e.track.dataRange=i,e.track.autoscale=!1,a.push(e.updateViews());await Promise.all(a)}}await Promise.all(s.map((t=>t.updateViews())))}}repaintViews(){for(let t of this.trackViews)t.repaintViews()}updateLocusSearchWidget(){if(!this.referenceFrameList)return;const t=this.referenceFrameList,e=this.calculateViewportWidth(this.referenceFrameList.length);for(let i of t)i.end=i.start+i.bpPerPixel*e;this.chromosomeSelectWidget.select.value=1===t.length?this.referenceFrameList[0].chr:"";const i=this.referenceFrameList.map((t=>t.getLocusString())).join(" ");this.$searchInput.val(i),this.fireEvent("locuschange",[this.referenceFrameList])}calculateViewportWidth(t){let{width:e}=this.columnContainer.getBoundingClientRect();return e-=50+this.getSampleNameViewportWidth()+14+12+28,e-=5*(t-1),Math.floor(e/t)}getCenterLineXOffset(){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleNameViewportWidth()+14+12+28,Math.floor(t/2+50)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(t,e,i){if(!this.referenceFrameList)return;const n=this.calculateViewportWidth(this.referenceFrameList.length);let r=i?[i]:this.referenceFrameList;for(let i of r)i.zoomWithScaleFactor(this,t,n,e)}async addMultiLocusPanel(t,e,i,n){if(!this.referenceFrameList)return;const r=this.calculateViewportWidth(1+this.referenceFrameList.length),s=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=s;const o=(i-e)/r,a=new Eb(this.genome,t,e,i,o),l=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,h=1+l,{$viewport:c}=this.trackViews[0].viewports[l],u=(t=>{const e=_e.div({class:"igv-column-shim"});ma(e,t);const i=_e.div({class:"igv-column"});return ma(i,e),i})(c.get(0).parentElement);if(h===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let t of this.trackViews){const e=tf(t,u,a);t.viewports.push(e)}}else{this.referenceFrameList.splice(h,0,a);for(let t of this.trackViews){const e=tf(t,u,a);t.viewports.splice(h,0,e)}}this.centerLineList=this.createCenterLineList(this.columnContainer),oy.call(this),await this.updateViews(!0)}async removeMultiLocusPanel(t){const e=this.referenceFrameList.indexOf(t),{$viewport:i}=this.trackViews[0].viewports[e];((t,e)=>{const i=0===t?e.nextElementSibling:e.previousElementSibling;e.remove(),i.remove()})(e,i.parent().get(0));for(let{viewports:t}of this.trackViews)t[e].dispose(),t.splice(e,1);if(this.referenceFrameList.splice(e,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let t of this.getRulerTrackView().viewports)t.dismissLocusLabel();const n=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(n)}async gotoMultilocusPanel(t){const e=this.referenceFrameList.indexOf(t);this.columnContainer.querySelectorAll(".igv-column").forEach(((t,i)=>{i===e||t.remove()})),this.columnContainer.querySelectorAll(".igv-column-shim").forEach((t=>t.remove()));for(let t of this.trackViews){const i=t.viewports[e];t.viewports.filter(((t,i)=>i!==e)).forEach((t=>t.dispose())),t.viewports=[i]}const i=this.calculateViewportWidth(1);t.bpPerPixel=(t.end-t.start)/i,this.referenceFrameList=[t],this.trackViews.forEach((({viewports:t})=>t.forEach((t=>t.setWidth(i))))),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(t){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=t;for(let{viewports:t}of this.trackViews)for(let i of t)i.setWidth(e);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(t,e,i){await this.search(t+":"+e+"-"+i)}async doSearch(t,e){const i=await this.search(t,e);return i||this.alert.present(new Error(`Unrecognized locus: ${t} `)),i}async search(t,e){const i=await async function(t,e){if(void 0===e||""===e.trim())return;(e&&"all"===e.trim().toLowerCase()||"*"===e)&&(e="all");const i=e.split(" ");let n=t.searchConfig||Mb,r=[];const s=async i=>{let r=function(t,e){const i=e.split("\t");if(i.length>=3)try{const e=t.genome.getChromosomeName(i[0]),n=parseInt(i[1].replace(/,/g,""),10)-1,r=parseInt(i[2].replace(/,/g,""),10);if(!isNaN(n)&&!isNaN(r))return{chr:e,start:n,end:r}}catch(t){}const n=e.split(":"),r=n[0];if("all"===r&&t.genome.getChromosome(r))return{chr:r,start:0,end:t.genome.getChromosome(r).bpLength};if(void 0!==t.genome.getChromosome(r)){const e={chr:t.genome.getChromosomeName(r),start:0,end:t.genome.getChromosome(r).bpLength};if(n.length>1){let i,r=n[1].split("-");if(r.length>2){if(!n[1].startsWith("-"))return;{const t=n[1].indexOf("-",1);t>0&&(r=[n[1].substring(0,t),n[1].substring(t+1)])}}if(i=r[0].replace(/,/g,""),isNaN(i))return;if(e.start=parseInt(i,10)-1,e.end=e.start+1,1===r.length&&(e.start-=20,e.end+=20),2===r.length){if(i=r[1].replace(/,/g,""),isNaN(i))return;if(e.end=parseInt(i,10),e.start<0&&!t.isSoftclipped()){const t=-e.start;e.start+=t,e.end+=t}}}return e}}(t,i);if(!r){const n=t.genome.featureDB.get(i.toUpperCase());n&&(r={chr:n.chr,start:n.start,end:n.end,gene:n.name,locusSearchString:e})}if(!r&&t.config&&!1!==t.config.search)try{r=await async function(t,e,i){let n=i.url.replace("$FEATURE$",e.toUpperCase());n.indexOf("$GENOME$")>-1&&(n=n.replace("$GENOME$",t.genome.id?t.genome.id:"hg19"));const r=i.timeout?{timeout:i.timeout}:void 0,s=function(t,e,i){let n;if(n="plain"===i.type?function(t,e){const i=[],n=[];return qi(e).forEach((function(t){""===t||i.push(t)})),i.forEach((function(e){var i,r,s,o,a=e.split("\t");a.length>=3&&(s=(r=a[1].split(":"))[1].split("-"),i=a[2].trim(),o={gene:a[0],chromosome:t.genome.getChromosomeName(r[0].trim()),start:parseInt(s[0].replace(/,/g,"")),end:parseInt(s[1].replace(/,/g,"")),type:"gtex"===i?"snp":"gene"},n.push(o))})),n}(t,e):JSON.parse(e),i.resultsField&&(n=n[i.resultsField]),n&&0!==n.length){const e=i.chromosomeField||"chromosome",r=i.startField||"start",s=i.endField||"end",o=i.coords||1;let a;a=Array.isArray(n)?n[0]:n,a.hasOwnProperty(e)&&a.hasOwnProperty(r)||console.error("Search service results must include chromosome and start fields: "+a);const l=a[e],h=t.genome.getChromosome(l);if(!h)return;const c=h.name;let u=a[r]-o,d=a[s];void 0===d&&(d=u+1);const f={chr:c,start:u,end:d},p=a.type?a.type:"gene";return i.geneField&&"gene"===p&&(f.gene=a[i.geneField]),i.snpField&&"snp"===p&&(f.snp=a[i.snpField]),f}}(t,await zo.loadString(n,r),i);return s&&(s.locusSearchString=e),s}(t,i,n)}catch(t){throw console.error(t),Error("Search service currently unavailable.")}return r};for(let t of i){const e=await s(t);e&&(e.locusSearchString=t,r.push(e))}if(0===r.length){const t=await s(e);t&&(t.locusSearchString=e,r.push(t))}return 0===r.length?void 0:r}(this,t);if(i&&i.length>0){this.referenceFrameList=function(t,e,i,n,r,s){return t.map((t=>{if(i&&t.gene&&(t.start=Math.max(0,t.start-i),t.end+=i),!s){const i=e.getChromosome(t.chr);ca(i.bpLength,t,n)}const o=new Eb(e,t.chr,t.start,t.end,(t.end-t.start)/r);return o.locusSearchString=t.locusSearchString,(t.gene||t.snp)&&(o.selection=new Tb(t.gene,t.snp)),o}))}(i,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(i.length),this.isSoftclipped());for(let t of this.trackViews)t.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(".igv-column-shim, .igv-column").forEach((t=>t.remove())),((t,e)=>{for(let i=0;i1&&i>0&&ga(_e.div({class:"igv-column-shim"}),n)}})(this.columnContainer.querySelector(".igv-sample-name-column"),this.referenceFrameList.length),this.centerLineList=this.createCenterLineList(this.columnContainer);for(let t of this.trackViews)t.addDOMToColumnContainer(this,this.columnContainer,this.referenceFrameList);return this.updateUIWithReferenceFrameList(),e||await this.updateViews(),!0}return!1}async loadSampleInformation(t){var e=t;Yi(t)&&(e=t.name),"fam"===e.substr(e.lastIndexOf(".")+1)&&(this.sampleInformation=await function(t,e){return(new Ab).loadPlinkFile(t,void 0)}(t))}on(t,e){this.eventHandlers[t]||(this.eventHandlers[t]=[]),this.eventHandlers[t].push(e)}un(t,e){this.off(t,e)}off(t,e){if(t)if(e){const i=this.eventHandlers[t];if(i&&0!==i.length){const n=i.indexOf(e);-1!==n&&this.eventHandlers[t].splice(n,1)}else console.warn("No handlers to remove for event: "+t)}else this.eventHandlers[t]=[];else this.eventHandlers={}}fireEvent(t,e,i){const n=this.eventHandlers[t];if(void 0===n||0===n.length)return;const r=i||window;return n.map((function(t){return t.apply(r,e)}))[0]}dispose(){this.removeMouseHandlers();for(let t of this.trackViews)t.dispose()}toJSON(){const t={version:"2.15.11"};if(void 0!==this.showSampleNames&&(t.showSampleNames=this.showSampleNames),200!==this.sampleNameViewportWidth&&(t.sampleNameViewportWidth=this.sampleNameViewportWidth),t.reference=this.genome.toJSON(),t.reference.fastaURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${t.reference.fastaURL.name}.`);if(t.reference.indexURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${t.reference.indexURL.name}.`);const e=[],i={};let n=!1,r=this.trackViews[0];for(let{referenceFrame:t}of r.viewports){const r=t.getLocusString();if(e.push(r),t.selection){const e={gene:t.selection.gene,snp:t.selection.snp};i[r]=e,n=!0}}t.locus=1===e.length?e[0]:e,n&&(t.gtexSelections=i),t.roi=this.roiManager.toJSON();const s=[],o=[];for(let{track:t}of this.trackViews)try{let e;e="function"==typeof t.getState?t.getState():t.config,e&&(e.browser&&delete e.browser,e.order=t.order,s.push(e))}catch(e){console.error(`Track: ${t.name}: ${e}`),o.push(`Track: ${t.name}: ${e}`)}if(o.length>0){let t=1,e="Errors encountered saving session:
";for(let i of o)e+=` (${t++}) ${i.toString()}
`;throw Error(e)}return t.tracks=s,t}compressedSession(){return function(t){const e=new Uint8Array(t.length);for(var i=0;i0?t.substring(0,e):t)+"?sessionURL=blob:"+this.compressedSession()}mouseDownOnViewport(t,e){var i;i=_e.pageCoordinates(t),this.vpMouseDown={viewport:e,lastMouseX:i.x,mouseDownX:i.x,lastMouseY:i.y,mouseDownY:i.y,referenceFrame:e.referenceFrame}}cancelTrackPan(){const t=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,t&&t.viewport.referenceFrame.start!==t.start&&(this.updateViews(),this.fireEvent("trackdragend"))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((t=>!0===t.track.showSoftClips))}startTrackDrag(t){this.dragTrack=t}updateTrackDrag(t){if(t&&this.dragTrack){const e=this.dragTrack,i=this.trackViews.indexOf(t),n=this.trackViews.indexOf(e),r=this.trackViews;r[i]=e,r[n]=t;const s=this.trackViews[i].track.order;this.trackViews[n].track.order=s;const o=r.length;let a=s;if(i0;t--){const e=r[t].track;if(!(e.order>=a))break;e.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=e.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent("trackorderchanged",[this.getTrackOrder()])):this.dragTrack=void 0}addMouseHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers()}removeMouseHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers()}addWindowResizeHandler(){this.boundWindowResizeHandler=oy.bind(this),window.addEventListener("resize",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener("resize",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=ly.bind(this),this.root.addEventListener("mouseup",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener("mouseup",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=ly.bind(this),this.root.addEventListener("mouseleave",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener("mouseleave",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=ay.bind(this),this.boundColumnContainerTouchMoveHandler=ay.bind(this),this.boundColumnContainerMouseLeaveHandler=ly.bind(this),this.boundColumnContainerMouseUpHandler=ly.bind(this),this.boundColumnContainerTouchEndHandler=ly.bind(this),this.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener("touchend",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener("touchend",this.boundColumnContainerTouchEndHandler)}static uncompressSession(t){let e;if(t.indexOf("/gzip;base64")>0){e=bo(t);let i="";for(let t of e)i+=String.fromCharCode(t);return i}return function(t){t=t.replace(/\./g,"+").replace(/_/g,"/").replace(/-/g,"=");const e=atob(t),i=[];for(let t=0;t{const r=t.data,s=r.mate;function o(t){t.chr=i.genome.getChromosomeName(t.refName);let e=!1;for(let n of i.referenceFrameList){const i=qu.fromLocusString(n.getLocusString());if(i.contains(t)){e=!0;break}if(i.overlaps(t)){n.extend(t),e=!0;break}}if(!e){const e=2e3,n=(t.start+t.end)/2;i.addMultiLocusPanel(t.chr,n-e,n+e)}}o(r),o(s)}})),this.circularViewControl=new Gb(this.$toggle_button_container.get(0),this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:wd(this.genome)}),this.circularViewVisible=e,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(t){this.circularView&&(this.circularView.visible=t,this.circularViewControl.setState(t))}}async function oy(){if(!this.referenceFrameList)return;const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList){const i=this.referenceFrameList.indexOf(e),{chr:n,genome:r}=e,{bpLength:s}=r.getChromosome(e.chr),o=e.toBP(t);ul.isWholeGenomeView(n)||o>s?e.bpPerPixel=s/t:e.end=e.start+e.toBP(t);for(let{viewports:e}of this.trackViews)e[i].setWidth(t)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function ay(t){t.preventDefault();const{x:e,y:i}=_e.pageCoordinates(t);if(this.vpMouseDown){const{viewport:t,referenceFrame:n}=this.vpMouseDown,r=Math.abs(e-this.vpMouseDown.mouseDownX)>Math.abs(i-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(r)this.vpMouseDown.mouseDownX&&Math.abs(e-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:t,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(i-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const e=t.$viewport.height(),i=t.trackView.maxViewportContentHeight();this.vpMouseDown.r=e/i}if(this.dragObject){const i=!this.isSoftclipped();let r=this.vpMouseDown.lastMouseX-e;n.shiftPixels(r,t.$viewport.width(),i)&&this.updateViews(),this.fireEvent("trackdrag")}if(this.isScrolling){const e=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-i);t.trackView.moveScroller(e)}this.vpMouseDown.lastMouseX=e,this.vpMouseDown.lastMouseY=i}}function ly(t){this.cancelTrackPan(),this.endTrackDrag()}function hy(t,e){for(let{viewports:i}of t)for(let t of i)t.$trackLabel&&(0===i.indexOf(t)&&!0===e?t.$trackLabel.show():t.$trackLabel.hide())}let cy=[];const uy=zo.setApiKey;!function(){var t=document.createElement("style");t.setAttribute("type","text/css"),t.innerHTML='.igv-navbar {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n box-sizing: border-box;\n width: 100%;\n color: #444;\n font-size: 12px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n line-height: 32px;\n padding-left: 8px;\n padding-right: 8px;\n margin-top: 2px;\n margin-bottom: 6px;\n height: 32px;\n border-style: solid;\n border-radius: 3px;\n border-width: thin;\n border-color: #bfbfbf;\n background-color: #f3f3f3;\n}\n.igv-navbar .igv-navbar-left-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 32px;\n line-height: 32px;\n}\n.igv-navbar .igv-navbar-left-container .igv-logo {\n width: 34px;\n height: 32px;\n margin-right: 8px;\n}\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\n height: 32px;\n margin-left: 4px;\n margin-right: 4px;\n user-select: none;\n line-height: 32px;\n vertical-align: middle;\n text-align: center;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 100%;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n height: 100%;\n width: 125px;\n margin-right: 4px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\n display: block;\n cursor: pointer;\n width: 100px;\n height: 75%;\n outline: none;\n font-size: 12px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n margin-left: 8px;\n height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n width: 210px;\n height: 22px;\n line-height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\n cursor: text;\n width: 85%;\n height: 22px;\n line-height: 22px;\n font-size: 12px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n text-align: left;\n padding-left: 8px;\n margin-right: 8px;\n outline: none;\n border-style: solid;\n border-radius: 3px;\n border-width: thin;\n border-color: #bfbfbf;\n background-color: white;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\n cursor: pointer;\n height: 16px;\n width: 16px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\n margin-left: 4px;\n user-select: none;\n}\n.igv-navbar .igv-navbar-right-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 32px;\n line-height: 32px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 100%;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div {\n margin-left: 0;\n margin-right: 4px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div:last-child {\n margin-left: 0;\n margin-right: 0;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-750 {\n display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\n color: #737373;\n font-size: 18px;\n height: 32px;\n line-height: 32px;\n margin-left: 8px;\n user-select: none;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\n cursor: pointer;\n margin-left: unset;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\n height: 24px;\n width: 24px;\n margin-left: unset;\n margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\n height: 24px;\n width: 24px;\n margin-left: 8px;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\n display: block;\n height: fit-content;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\n display: block;\n width: 125px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\n display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\n color: #737373;\n font-size: 18px;\n height: 32px;\n line-height: 32px;\n margin-left: 8px;\n user-select: none;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\n cursor: pointer;\n margin-left: unset;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\n height: 24px;\n width: 24px;\n margin-left: unset;\n margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\n height: 24px;\n width: 24px;\n margin-left: 8px;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\n width: 0;\n height: 0;\n display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\n width: 0;\n height: 0;\n display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\n display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\n display: none;\n}\n\n.igv-navbar-button {\n display: block;\n box-sizing: unset;\n padding-left: 6px;\n padding-right: 6px;\n height: 18px;\n text-transform: capitalize;\n user-select: none;\n line-height: 18px;\n text-align: center;\n vertical-align: middle;\n font-family: "Open Sans", sans-serif;\n font-size: 11px;\n font-weight: 200;\n color: #737373;\n background-color: #f3f3f3;\n border-color: #737373;\n border-style: solid;\n border-width: thin;\n border-radius: 6px;\n}\n\n.igv-navbar-button-clicked {\n color: white;\n background-color: #737373;\n}\n\n.igv-navbar-button:hover {\n cursor: pointer;\n}\n\n.igv-zoom-in-notice-container {\n z-index: 1024;\n position: absolute;\n top: 8px;\n left: 50%;\n transform: translate(-50%, 0%);\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n background-color: white;\n}\n.igv-zoom-in-notice-container > div {\n padding-left: 4px;\n padding-right: 4px;\n padding-top: 2px;\n padding-bottom: 2px;\n width: 100%;\n height: 100%;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n color: #3f3f3f;\n}\n\n.igv-zoom-in-notice {\n position: absolute;\n top: 10px;\n left: 50%;\n}\n.igv-zoom-in-notice div {\n position: relative;\n left: -50%;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n color: #3f3f3f;\n background-color: rgba(255, 255, 255, 0.51);\n z-index: 64;\n}\n\n.igv-container-spinner {\n position: absolute;\n top: 90%;\n left: 50%;\n transform: translate(-50%, -50%);\n z-index: 1024;\n width: 24px;\n height: 24px;\n pointer-events: none;\n color: #737373;\n}\n\n.igv-multi-locus-close-button {\n position: absolute;\n top: 2px;\n right: 0;\n padding-left: 2px;\n padding-right: 2px;\n width: 12px;\n height: 12px;\n color: #666666;\n background-color: white;\n z-index: 1000;\n}\n.igv-multi-locus-close-button > svg {\n vertical-align: top;\n}\n\n.igv-multi-locus-close-button:hover {\n cursor: pointer;\n color: #434343;\n}\n\n.igv-multi-locus-ruler-label {\n z-index: 64;\n position: absolute;\n top: 2px;\n left: 0;\n width: 100%;\n height: 12px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n}\n.igv-multi-locus-ruler-label > div {\n font-family: "Open Sans", sans-serif;\n font-size: 12px;\n color: rgb(16, 16, 16);\n background-color: white;\n}\n.igv-multi-locus-ruler-label > div {\n cursor: pointer;\n}\n\n.igv-multi-locus-ruler-label-square-dot {\n z-index: 64;\n position: absolute;\n left: 50%;\n top: 5%;\n transform: translate(-50%, 0%);\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\n width: 14px;\n height: 14px;\n}\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\n margin-left: 16px;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n color: rgb(16, 16, 16);\n}\n\n.igv-ruler-sweeper {\n display: none;\n pointer-events: none;\n position: absolute;\n top: 26px;\n bottom: 0;\n left: 0;\n width: 0;\n z-index: 99999;\n background-color: rgba(68, 134, 247, 0.25);\n}\n\n.igv-ruler-tooltip {\n pointer-events: none;\n z-index: 128;\n position: absolute;\n top: 0;\n left: 0;\n width: 1px;\n height: 32px;\n background-color: transparent;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ruler-tooltip > div {\n pointer-events: none;\n width: 128px;\n height: auto;\n padding: 1px;\n color: #373737;\n font-size: 10px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n background-color: white;\n border-style: solid;\n border-width: thin;\n border-color: #373737;\n}\n\n.igv-track-label {\n position: absolute;\n left: 8px;\n top: 8px;\n width: auto;\n height: auto;\n max-width: 50%;\n padding-left: 4px;\n padding-right: 4px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n text-align: center;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n border-color: #444;\n border-radius: 2px;\n border-style: solid;\n border-width: thin;\n background-color: white;\n z-index: 128;\n cursor: pointer;\n}\n\n.igv-track-label:hover,\n.igv-track-label:focus,\n.igv-track-label:active {\n background-color: #e8e8e8;\n}\n\n.igv-track-label-popup-shim {\n padding-left: 8px;\n padding-right: 8px;\n padding-top: 4px;\n}\n\n.igv-center-line {\n display: none;\n pointer-events: none;\n position: absolute;\n top: 0;\n bottom: 0;\n left: 50%;\n transform: translateX(-50%);\n z-index: 8;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n border-left-style: dashed;\n border-left-width: thin;\n border-right-style: dashed;\n border-right-width: thin;\n}\n\n.igv-center-line-wide {\n background-color: rgba(0, 0, 0, 0);\n border-left-color: rgba(127, 127, 127, 0.51);\n border-right-color: rgba(127, 127, 127, 0.51);\n}\n\n.igv-center-line-thin {\n background-color: rgba(0, 0, 0, 0);\n border-left-color: rgba(127, 127, 127, 0.51);\n border-right-color: rgba(0, 0, 0, 0);\n}\n\n.igv-cursor-guide-horizontal {\n display: none;\n pointer-events: none;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n position: absolute;\n left: 0;\n right: 0;\n top: 50%;\n height: 1px;\n z-index: 1;\n margin-left: 50px;\n margin-right: 54px;\n border-top-style: dotted;\n border-top-width: thin;\n border-top-color: rgba(127, 127, 127, 0.76);\n}\n\n.igv-cursor-guide-vertical {\n pointer-events: none;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n position: absolute;\n top: 0;\n bottom: 0;\n left: 50%;\n width: 1px;\n z-index: 1;\n border-left-style: dotted;\n border-left-width: thin;\n border-left-color: rgba(127, 127, 127, 0.76);\n display: none;\n}\n\n.igv-user-feedback {\n position: fixed;\n top: 50%;\n left: 50%;\n transform: translate(-50%, -50%);\n width: 512px;\n height: 360px;\n z-index: 2048;\n background-color: white;\n border-color: #a2a2a2;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n color: #444;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-user-feedback div:first-child {\n position: relative;\n height: 24px;\n width: 100%;\n background-color: white;\n border-bottom-color: #a2a2a2;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n position: absolute;\n top: 2px;\n width: 16px;\n height: 16px;\n background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n cursor: pointer;\n right: 8px;\n}\n.igv-user-feedback div:last-child {\n width: 100%;\n height: calc(100% - 24px);\n border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n width: auto;\n height: auto;\n margin: 8px;\n}\n\n.igv-generic-dialog-container {\n position: absolute;\n top: 0;\n left: 0;\n width: 300px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n z-index: 2048;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\n color: #373737;\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin-top: 8px;\n padding-left: 8px;\n overflow-wrap: break-word;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\n margin-top: 8px;\n width: 95%;\n height: 24px;\n color: #373737;\n line-height: 24px;\n padding-left: 8px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\n width: 30%;\n height: 100%;\n font-size: 16px;\n text-align: right;\n padding-right: 8px;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n width: 50%;\n font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input {\n margin-top: 8px;\n width: calc(100% - 16px);\n height: 24px;\n color: #373737;\n line-height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\n width: 100%;\n height: 28px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\n margin-top: 32px;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\n margin-left: 32px;\n margin-right: 0;\n background-color: #5ea4e0;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\n margin-left: 0;\n margin-right: 32px;\n background-color: #c4c4c4;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f;\n}\n\n.igv-generic-container {\n position: absolute;\n top: 0;\n left: 0;\n z-index: 2048;\n background-color: white;\n cursor: pointer;\n display: flex;\n flex-direction: row;\n flex-wrap: wrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-generic-container div:first-child {\n cursor: move;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n height: 24px;\n width: 100%;\n background-color: #dddddd;\n}\n.igv-generic-container div:first-child i {\n display: block;\n color: #5f5f5f;\n cursor: pointer;\n width: 14px;\n height: 14px;\n margin-right: 8px;\n margin-bottom: 4px;\n}\n\n.igv-menu-popup {\n position: absolute;\n top: 0;\n left: 0;\n width: max-content;\n z-index: 4096;\n cursor: pointer;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n color: #4b4b4b;\n background: white;\n border-radius: 4px;\n border-color: #7F7F7F;\n border-style: solid;\n border-width: thin;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-end;\n text-align: left;\n}\n.igv-menu-popup > div:not(:first-child) {\n width: 100%;\n}\n.igv-menu-popup > div:not(:first-child) > div {\n background: white;\n}\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\n padding-left: 4px;\n padding-right: 4px;\n}\n.igv-menu-popup > div:not(:first-child) > div:last-child {\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-color: transparent;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-menu-popup > div:not(:first-child) > div:hover {\n background: #efefef;\n}\n\n.igv-menu-popup-shim {\n padding-left: 8px;\n padding-right: 8px;\n padding-bottom: 1px;\n padding-top: 1px;\n}\n\n.igv-menu-popup-header {\n position: relative;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-color: transparent;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-menu-popup-header div {\n margin-right: 4px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-menu-popup-header div:hover {\n cursor: pointer;\n color: #444;\n}\n\n.igv-menu-popup-check-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n width: 100%;\n height: 20px;\n margin-right: 4px;\n background-color: transparent;\n}\n.igv-menu-popup-check-container div {\n padding-top: 2px;\n padding-left: 8px;\n}\n.igv-menu-popup-check-container div:first-child {\n position: relative;\n width: 12px;\n height: 12px;\n}\n.igv-menu-popup-check-container div:first-child svg {\n position: absolute;\n width: 12px;\n height: 12px;\n}\n\n.igv-user-feedback {\n position: fixed;\n top: 50%;\n left: 50%;\n transform: translate(-50%, -50%);\n width: 512px;\n height: 360px;\n z-index: 2048;\n background-color: white;\n border-color: #a2a2a2;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n color: #444;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-user-feedback div:first-child {\n position: relative;\n height: 24px;\n width: 100%;\n background-color: white;\n border-bottom-color: #a2a2a2;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n position: absolute;\n top: 2px;\n width: 16px;\n height: 16px;\n background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n cursor: pointer;\n right: 8px;\n}\n.igv-user-feedback div:last-child {\n width: 100%;\n height: calc(100% - 24px);\n border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n width: auto;\n height: auto;\n margin: 8px;\n}\n\n.igv-loading-spinner-container {\n z-index: 1024;\n position: absolute;\n top: 50%;\n left: 50%;\n transform: translate(-50%, -50%);\n width: 32px;\n height: 32px;\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n}\n.igv-loading-spinner-container > div {\n box-sizing: border-box;\n width: 100%;\n height: 100%;\n border-radius: 50%;\n border: 4px solid rgba(128, 128, 128, 0.5);\n border-top-color: rgb(255, 255, 255);\n animation: spin 1s ease-in-out infinite;\n -webkit-animation: spin 1s ease-in-out infinite;\n}\n\n@keyframes spin {\n to {\n -webkit-transform: rotate(360deg);\n transform: rotate(360deg);\n }\n}\n@-webkit-keyframes spin {\n to {\n -webkit-transform: rotate(360deg);\n transform: rotate(360deg);\n }\n}\n.igv-roi-menu-next-gen {\n position: absolute;\n z-index: 512;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n color: #4b4b4b;\n background-color: white;\n width: 192px;\n border-radius: 4px;\n border-color: #7F7F7F;\n border-style: solid;\n border-width: thin;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-menu-next-gen > div:first-child {\n height: 24px;\n border-top-color: transparent;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-roi-menu-next-gen > div:first-child > div {\n margin-right: 4px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-roi-menu-next-gen > div:first-child > div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-roi-menu-next-gen > div:last-child {\n background-color: white;\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-color: transparent;\n border-bottom-style: solid;\n border-bottom-width: 0;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n text-align: start;\n vertical-align: middle;\n}\n.igv-roi-menu-next-gen > div:last-child > div {\n height: 24px;\n padding-left: 4px;\n border-bottom-style: solid;\n border-bottom-width: thin;\n border-bottom-color: #7f7f7f;\n}\n.igv-roi-menu-next-gen > div:last-child > div:not(:first-child):hover {\n background-color: rgba(127, 127, 127, 0.1);\n}\n.igv-roi-menu-next-gen > div:last-child div:first-child {\n font-style: italic;\n text-align: center;\n padding-right: 4px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n}\n.igv-roi-menu-next-gen > div:last-child > div:last-child {\n border-bottom-width: 0;\n border-bottom-color: transparent;\n}\n\n.igv-roi-placeholder {\n font-style: normal;\n color: rgba(75, 75, 75, 0.6);\n}\n\n.igv-roi-table {\n position: absolute;\n z-index: 1024;\n width: min-content;\n max-width: 1600px;\n border-color: #7f7f7f;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: 12px;\n font-weight: 400;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n cursor: default;\n}\n.igv-roi-table > div {\n height: 24px;\n font-size: 14px;\n text-align: start;\n vertical-align: middle;\n line-height: 24px;\n}\n.igv-roi-table > div:first-child {\n border-color: transparent;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-top-width: 0;\n border-bottom-color: #7f7f7f;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n cursor: move;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n}\n.igv-roi-table > div:first-child > div:first-child {\n text-align: center;\n white-space: nowrap;\n text-overflow: ellipsis;\n overflow: hidden;\n margin-left: 4px;\n margin-right: 4px;\n width: calc(100% - 4px - 12px);\n}\n.igv-roi-table > div:first-child > div:last-child {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7f7f7f;\n}\n.igv-roi-table > div:first-child > div:last-child > svg {\n display: block;\n}\n.igv-roi-table > div:first-child > div:last-child:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-roi-table > .igv-roi-table-description {\n padding: 4px;\n margin-left: 4px;\n word-break: break-all;\n overflow-y: auto;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n background-color: transparent;\n}\n.igv-roi-table > .igv-roi-table-goto-explainer {\n margin-top: 5px;\n margin-left: 4px;\n color: #7F7F7F;\n font-style: italic;\n height: 24px;\n border-top: solid lightgray;\n background-color: transparent;\n}\n.igv-roi-table > .igv-roi-table-column-titles {\n height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: stretch;\n align-items: stretch;\n padding-right: 16px;\n background-color: white;\n border-top-color: #7f7f7f;\n border-top-style: solid;\n border-top-width: thin;\n border-bottom-color: #7f7f7f;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div {\n font-size: 14px;\n vertical-align: middle;\n line-height: 24px;\n text-align: left;\n margin-left: 4px;\n height: 24px;\n overflow: hidden;\n text-overflow: ellipsis;\n border-right-color: #7f7f7f;\n border-right-style: solid;\n border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\n border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container {\n overflow: auto;\n resize: both;\n max-width: 1600px;\n height: 360px;\n background-color: transparent;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\n height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: stretch;\n align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\n font-size: 14px;\n vertical-align: middle;\n line-height: 24px;\n text-align: left;\n margin-left: 4px;\n height: 24px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n border-right-color: transparent;\n border-right-style: solid;\n border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\n border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table > div:last-child {\n height: 32px;\n line-height: 32px;\n border-top-color: #7f7f7f;\n border-top-style: solid;\n border-top-width: thin;\n border-bottom-color: transparent;\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-width: 0;\n background-color: #eee;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n\n.igv-roi-table-row-selected {\n background-color: rgba(0, 0, 0, 0.125);\n}\n\n.igv-roi-table-button {\n cursor: pointer;\n height: 20px;\n user-select: none;\n line-height: 20px;\n text-align: center;\n vertical-align: middle;\n font-family: "Open Sans", sans-serif;\n font-size: 13px;\n font-weight: 400;\n color: black;\n padding-left: 6px;\n padding-right: 6px;\n background-color: rgb(239, 239, 239);\n border-color: black;\n border-style: solid;\n border-width: thin;\n border-radius: 3px;\n}\n\n.igv-roi-table-button:hover {\n font-weight: 400;\n background-color: rgba(0, 0, 0, 0.13);\n}\n\n.igv-roi-region {\n z-index: 64;\n position: absolute;\n top: 0;\n bottom: 0;\n pointer-events: none;\n overflow: visible;\n margin-top: 44px;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-region > div {\n position: relative;\n width: 100%;\n height: 8px;\n pointer-events: auto;\n}\n\n.igv-roi-menu {\n position: absolute;\n z-index: 1024;\n width: 144px;\n border-color: #7f7f7f;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-menu > div:not(:last-child) {\n border-bottom-color: rgba(128, 128, 128, 0.5);\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-roi-menu > div:first-child {\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-top-color: transparent;\n border-top-style: solid;\n border-top-width: 0;\n}\n.igv-roi-menu > div:last-child {\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-color: transparent;\n border-bottom-style: solid;\n border-bottom-width: 0;\n}\n\n.igv-roi-menu-row {\n height: 24px;\n padding-left: 8px;\n font-size: small;\n text-align: start;\n vertical-align: middle;\n line-height: 24px;\n background-color: white;\n}\n\n.igv-roi-menu-row-edit-description {\n width: -webkit-fill-available;\n font-size: small;\n text-align: start;\n vertical-align: middle;\n background-color: white;\n padding-left: 4px;\n padding-right: 4px;\n padding-bottom: 4px;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: stretch;\n align-items: stretch;\n}\n.igv-roi-menu-row-edit-description > label {\n margin-left: 2px;\n margin-bottom: 0;\n display: block;\n width: -webkit-fill-available;\n}\n.igv-roi-menu-row-edit-description > input {\n display: block;\n margin-left: 2px;\n margin-right: 2px;\n margin-bottom: 1px;\n width: -webkit-fill-available;\n}\n\n.igv-container {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n padding-top: 4px;\n user-select: none;\n -webkit-user-select: none;\n -ms-user-select: none;\n}\n\n.igv-viewport {\n position: relative;\n margin-top: 5px;\n line-height: 1;\n overflow-x: hidden;\n overflow-y: hidden;\n}\n\n.igv-viewport-content {\n position: relative;\n width: 100%;\n}\n.igv-viewport-content > canvas {\n position: relative;\n display: block;\n}\n\n.igv-column-container {\n position: relative;\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n width: 100%;\n}\n\n.igv-column-shim {\n width: 1px;\n margin-left: 2px;\n margin-right: 2px;\n background-color: #545453;\n}\n\n.igv-column {\n position: relative;\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n}\n\n.igv-axis-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 50px;\n}\n.igv-axis-column > div {\n margin-top: 5px;\n width: 100%;\n}\n\n.igv-sample-name-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n}\n\n.igv-scrollbar-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 14px;\n}\n.igv-scrollbar-column > div {\n position: relative;\n margin-top: 5px;\n width: 14px;\n}\n.igv-scrollbar-column > div > div {\n cursor: pointer;\n position: absolute;\n top: 0;\n left: 2px;\n width: 8px;\n border-width: 1px;\n border-style: solid;\n border-color: #c4c4c4;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n}\n.igv-scrollbar-column > div > div:hover {\n background-color: #c4c4c4;\n}\n\n.igv-track-drag-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 12px;\n background-color: white;\n}\n.igv-track-drag-column > .igv-track-drag-handle {\n z-index: 512;\n position: relative;\n cursor: pointer;\n margin-top: 5px;\n width: 100%;\n border-style: solid;\n border-width: 0;\n border-top-right-radius: 6px;\n border-bottom-right-radius: 6px;\n background-color: #c4c4c4;\n}\n.igv-track-drag-column .igv-track-drag-handle-hover {\n background-color: #787878;\n}\n.igv-track-drag-column > .igv-track-drag-shim {\n position: relative;\n margin-top: 5px;\n width: 100%;\n border-style: solid;\n border-width: 0;\n}\n\n.igv-gear-menu-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 28px;\n}\n.igv-gear-menu-column > div {\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n margin-top: 5px;\n width: 100%;\n background: white;\n}\n.igv-gear-menu-column > div > div {\n position: relative;\n margin-top: 4px;\n width: 16px;\n height: 16px;\n color: #7F7F7F;\n}\n.igv-gear-menu-column > div > div:hover {\n cursor: pointer;\n color: #444;\n}\n\n/*# sourceMappingURL=dom.css.map */\n',document.head.append(t)}();const dy=zo.oauth;var fy={TrackUtils:Ia,IGVGraphics:na,MenuUtils:Ui,DataRangeDialog:Hi,createTrack:async function(t,e){return await sy.prototype.createTrack.call(e,t)},createBrowser:async function(t,e){void 0===e&&(e={}),ul.KNOWN_GENOMES||await ul.initializeGenomes(e),function(t){void 0===t.minimumBases&&(t.minimumBases=40),void 0===t.showIdeogram&&(t.showIdeogram=!0),void 0===t.showCircularView&&(t.showCircularView=!1),void 0===t.showCircularViewButton&&(t.showCircularViewButton=!1),void 0===t.showTrackLabelButton&&(t.showTrackLabelButton=!0),void 0===t.showTrackLabels&&(t.showTrackLabels=!0),void 0===t.showROITableButton&&(t.showROITableButton=!1),void 0===t.showROITable&&(t.showROITable=!1),void 0===t.showCursorTrackingGuideButton&&(t.showCursorTrackingGuideButton=!0),void 0===t.showCursorGuide&&(t.showCursorGuide=t.showCursorTrackingGuide||!1),void 0===t.showCenterGuideButton&&(t.showCenterGuideButton=!0),void 0===t.showCenterGuide&&(t.showCenterGuide=!1),void 0===t.showSampleNames&&(t.showSampleNames=!1),void 0===t.showSVGButton&&(t.showSVGButton=!0),void 0===t.showControls&&(t.showControls=!0),void 0===t.showNavigation&&(t.showNavigation=!0),void 0===t.showRuler&&(t.showRuler=!0),void 0===t.flanking&&(t.flanking=1e3),void 0===t.pairsSupported&&(t.pairsSupported=!0),t.tracks||(t.tracks=[])}(e),e.queryParametersSupported&&function(t){var e,i,n,r,s,o,a,l;let h,c,u;if({},e=(o=window.location.href).indexOf("?"),i=o.lastIndexOf("#"),e>=0)for(i<0&&(i=o.length),n=e+1;ne&&(i.indexURL=c[e]),u&&u.length>e&&(i.name=u[e]),t.tracks.push(i)}}}(e),e.apiKey&&zo.setApiKey(e.apiKey),e.oauthToken&&zo.setOauthToken(e.oauthToken),e.clientId&&!Ro()&&await async function(t){if(!google.accounts.oauth2.initTokenClient)throw new Error("Google accounts token client not loaded (https://accounts.google.com/gsi/client)");if(Ro())throw new Error("Google 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Uint32Array([0]),t._nullCount=-1,t[Symbol.isConcatSpreadable]=!0,t.isValid=mi(gi),t.get=mi(Ke.getVisitFn(h.Struct)),t.set=bi(Ce.getVisitFn(h.Struct)),t.indexOf=yi(Ei.getVisitFn(h.Struct)),t.getByteLength=mi(Pi.getVisitFn(h.Struct)),"Table"))(yn.prototype);class vn{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}offset(){return this.bb.readInt64(this.bb_pos)}metaDataLength(){return this.bb.readInt32(this.bb_pos+8)}bodyLength(){return this.bb.readInt64(this.bb_pos+16)}static sizeOf(){return 24}static createBlock(t,e,i,n){return t.prep(8,24),t.writeInt64(n),t.pad(4),t.writeInt32(i),t.writeInt64(e),t.offset()}}const wn=new Int32Array(2),_n=new Float32Array(wn.buffer),xn=new Float64Array(wn.buffer),kn=1===new Uint16Array(new Uint8Array([1,0]).buffer)[0];class Sn{constructor(t,e){this.low=0|t,this.high=0|e}static create(t,e){return 0==t&&0==e?Sn.ZERO:new Sn(t,e)}toFloat64(){return(this.low>>>0)+4294967296*this.high}equals(t){return this.low==t.low&&this.high==t.high}}var Cn,An,Tn,In,En;Sn.ZERO=new Sn(0,0),function(t){t[t.UTF8_BYTES=1]="UTF8_BYTES",t[t.UTF16_STRING=2]="UTF16_STRING"}(Cn||(Cn={}));class Mn{constructor(t){this.bytes_=t,this.position_=0}static allocate(t){return new Mn(new Uint8Array(t))}clear(){this.position_=0}bytes(){return this.bytes_}position(){return this.position_}setPosition(t){this.position_=t}capacity(){return this.bytes_.length}readInt8(t){return this.readUint8(t)<<24>>24}readUint8(t){return this.bytes_[t]}readInt16(t){return this.readUint16(t)<<16>>16}readUint16(t){return this.bytes_[t]|this.bytes_[t+1]<<8}readInt32(t){return this.bytes_[t]|this.bytes_[t+1]<<8|this.bytes_[t+2]<<16|this.bytes_[t+3]<<24}readUint32(t){return this.readInt32(t)>>>0}readInt64(t){return new Sn(this.readInt32(t),this.readInt32(t+4))}readUint64(t){return new Sn(this.readUint32(t),this.readUint32(t+4))}readFloat32(t){return wn[0]=this.readInt32(t),_n[0]}readFloat64(t){return wn[kn?0:1]=this.readInt32(t),wn[kn?1:0]=this.readInt32(t+4),xn[0]}writeInt8(t,e){this.bytes_[t]=e}writeUint8(t,e){this.bytes_[t]=e}writeInt16(t,e){this.bytes_[t]=e,this.bytes_[t+1]=e>>8}writeUint16(t,e){this.bytes_[t]=e,this.bytes_[t+1]=e>>8}writeInt32(t,e){this.bytes_[t]=e,this.bytes_[t+1]=e>>8,this.bytes_[t+2]=e>>16,this.bytes_[t+3]=e>>24}writeUint32(t,e){this.bytes_[t]=e,this.bytes_[t+1]=e>>8,this.bytes_[t+2]=e>>16,this.bytes_[t+3]=e>>24}writeInt64(t,e){this.writeInt32(t,e.low),this.writeInt32(t+4,e.high)}writeUint64(t,e){this.writeUint32(t,e.low),this.writeUint32(t+4,e.high)}writeFloat32(t,e){_n[0]=e,this.writeInt32(t,wn[0])}writeFloat64(t,e){xn[0]=e,this.writeInt32(t,wn[kn?0:1]),this.writeInt32(t+4,wn[kn?1:0])}getBufferIdentifier(){if(this.bytes_.length>10),56320+(1023&e)))}return n}__union_with_string(t,e){return"string"==typeof t?this.__string(e):this.__union(t,e)}__indirect(t){return t+this.readInt32(t)}__vector(t){return t+this.readInt32(t)+4}__vector_len(t){return this.readInt32(t+this.readInt32(t))}__has_identifier(t){if(4!=t.length)throw new Error("FlatBuffers: file identifier must be length 4");for(let e=0;e<4;e++)if(t.charCodeAt(e)!=this.readInt8(this.position()+4+e))return!1;return!0}createLong(t,e){return Sn.create(t,e)}createScalarList(t,e){const i=[];for(let n=0;nthis.minalign&&(this.minalign=t);const i=1+~(this.bb.capacity()-this.space+e)&t-1;for(;this.space=0&&0==this.vtable[e];e--);const i=e+1;for(;e>=0;e--)this.addInt16(0!=this.vtable[e]?t-this.vtable[e]:0);this.addInt16(t-this.object_start);const n=2*(i+2);this.addInt16(n);let r=0;const s=this.space;t:for(e=0;e=0;e--)this.writeInt8(t.charCodeAt(e))}this.prep(this.minalign,4+n),this.addOffset(t),n&&this.addInt32(this.bb.capacity()-this.space),this.bb.setPosition(this.space)}finishSizePrefixed(t,e){this.finish(t,e,!0)}requiredField(t,e){const i=this.bb.capacity()-t,n=i-this.bb.readInt32(i);if(0==this.bb.readInt16(n+e))throw new Error("FlatBuffers: field "+e+" must be set")}startVector(t,e,i){this.notNested(),this.vector_num_elems=e,this.prep(4,t*e),this.prep(i,t*e)}endVector(){return this.writeInt32(this.vector_num_elems),this.offset()}createSharedString(t){if(!t)return 0;if(this.string_maps||(this.string_maps=new Map),this.string_maps.has(t))return this.string_maps.get(t);const e=this.createString(t);return this.string_maps.set(t,e),e}createString(t){if(!t)return 0;let e;if(t instanceof Uint8Array)e=t;else{e=[];let i=0;for(;i=56320?r:(r<<10)+t.charCodeAt(i++)+-56613888,n<128?e.push(n):(n<2048?e.push(n>>6&31|192):(n<65536?e.push(n>>12&15|224):e.push(n>>18&7|240,n>>12&63|128),e.push(n>>6&63|128)),e.push(63&n|128))}}this.addInt8(0),this.startVector(1,e.length,1),this.bb.setPosition(this.space-=e.length);for(let t=0,i=this.space,n=this.bb.bytes();t=0;i--)t.addOffset(e[i]);return t.endVector()}static startChildrenVector(t,e){t.startVector(4,e,4)}static addCustomMetadata(t,e){t.addFieldOffset(6,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static endField(t){return t.endObject()}}class On{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsSchema(t,e){return(e||new On).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsSchema(t,e){return t.setPosition(t.position()+4),(e||new On).__init(t.readInt32(t.position())+t.position(),t)}endianness(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):Tn.Little}fields(t,e){const i=this.bb.__offset(this.bb_pos,6);return i?(e||new Fn).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}fieldsLength(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.__vector_len(this.bb_pos+t):0}customMetadata(t,e){const i=this.bb.__offset(this.bb_pos,8);return i?(e||new Ln).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}customMetadataLength(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.__vector_len(this.bb_pos+t):0}features(t){const e=this.bb.__offset(this.bb_pos,10);return e?this.bb.readInt64(this.bb.__vector(this.bb_pos+e)+8*t):this.bb.createLong(0,0)}featuresLength(){const t=this.bb.__offset(this.bb_pos,10);return t?this.bb.__vector_len(this.bb_pos+t):0}static startSchema(t){t.startObject(4)}static addEndianness(t,e){t.addFieldInt16(0,e,Tn.Little)}static addFields(t,e){t.addFieldOffset(1,e,0)}static createFieldsVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startFieldsVector(t,e){t.startVector(4,e,4)}static addCustomMetadata(t,e){t.addFieldOffset(2,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static addFeatures(t,e){t.addFieldOffset(3,e,0)}static createFeaturesVector(t,e){t.startVector(8,e.length,8);for(let i=e.length-1;i>=0;i--)t.addInt64(e[i]);return t.endVector()}static startFeaturesVector(t,e){t.startVector(8,e,8)}static endSchema(t){return t.endObject()}static finishSchemaBuffer(t,e){t.finish(e)}static finishSizePrefixedSchemaBuffer(t,e){t.finish(e,void 0,!0)}static createSchema(t,e,i,n,r){return On.startSchema(t),On.addEndianness(t,e),On.addFields(t,i),On.addCustomMetadata(t,n),On.addFeatures(t,r),On.endSchema(t)}}class Dn{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFooter(t,e){return(e||new Dn).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFooter(t,e){return t.setPosition(t.position()+4),(e||new Dn).__init(t.readInt32(t.position())+t.position(),t)}version(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):An.V1}schema(t){const e=this.bb.__offset(this.bb_pos,6);return e?(t||new On).__init(this.bb.__indirect(this.bb_pos+e),this.bb):null}dictionaries(t,e){const i=this.bb.__offset(this.bb_pos,8);return i?(e||new vn).__init(this.bb.__vector(this.bb_pos+i)+24*t,this.bb):null}dictionariesLength(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.__vector_len(this.bb_pos+t):0}recordBatches(t,e){const i=this.bb.__offset(this.bb_pos,10);return i?(e||new vn).__init(this.bb.__vector(this.bb_pos+i)+24*t,this.bb):null}recordBatchesLength(){const t=this.bb.__offset(this.bb_pos,10);return t?this.bb.__vector_len(this.bb_pos+t):0}customMetadata(t,e){const i=this.bb.__offset(this.bb_pos,12);return i?(e||new Ln).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}customMetadataLength(){const t=this.bb.__offset(this.bb_pos,12);return t?this.bb.__vector_len(this.bb_pos+t):0}static startFooter(t){t.startObject(5)}static addVersion(t,e){t.addFieldInt16(0,e,An.V1)}static addSchema(t,e){t.addFieldOffset(1,e,0)}static addDictionaries(t,e){t.addFieldOffset(2,e,0)}static startDictionariesVector(t,e){t.startVector(24,e,8)}static addRecordBatches(t,e){t.addFieldOffset(3,e,0)}static startRecordBatchesVector(t,e){t.startVector(24,e,8)}static addCustomMetadata(t,e){t.addFieldOffset(4,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static endFooter(t){return t.endObject()}static finishFooterBuffer(t,e){t.finish(e)}static finishSizePrefixedFooterBuffer(t,e){t.finish(e,void 0,!0)}}var Pn=Sn,zn=Rn,Un=Mn;class Vn{constructor(t,i=e.V4,n,r){this.schema=t,this.version=i,n&&(this._recordBatches=n),r&&(this._dictionaryBatches=r)}static decode(t){t=new Un(Y(t));const e=Dn.getRootAsFooter(t),i=Gi.decode(e.schema());return new Hn(i,e)}static encode(t){const i=new zn,n=Gi.encode(i,t.schema);Dn.startRecordBatchesVector(i,t.numRecordBatches);for(const e of[...t.recordBatches()].slice().reverse())jn.encode(i,e);const r=i.endVector();Dn.startDictionariesVector(i,t.numDictionaries);for(const e of[...t.dictionaryBatches()].slice().reverse())jn.encode(i,e);const s=i.endVector();return Dn.startFooter(i),Dn.addSchema(i,n),Dn.addVersion(i,e.V4),Dn.addRecordBatches(i,r),Dn.addDictionaries(i,s),Dn.finishFooterBuffer(i,Dn.endFooter(i)),i.asUint8Array()}get numRecordBatches(){return this._recordBatches.length}get numDictionaries(){return this._dictionaryBatches.length}*recordBatches(){for(let t,e=-1,i=this.numRecordBatches;++e=0&&t=0&&t=0&&t=0&&tqn(function*(t){let e,i,n,r,s=!1,o=[],a=0;({cmd:n,size:r}=yield null);const l=(h=t,function*(t,e){const i=function*(t){yield t},n="string"==typeof e||ArrayBuffer.isView(e)||e instanceof ArrayBuffer||e instanceof $?i(e):S(e)?e:i(e);return yield*Q(function*(e){let i=null;do{i=e.next(yield 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Wn{constructor(t){this.source=t,this.reader=null,this.reader=this.source.getReader(),this.reader.closed.catch((()=>{}))}get closed(){return this.reader?this.reader.closed.catch((()=>{})):Promise.resolve()}releaseLock(){this.reader&&this.reader.releaseLock(),this.reader=null}cancel(t){return F(this,void 0,void 0,(function*(){const{reader:e,source:i}=this;e&&(yield e.cancel(t).catch((()=>{}))),i&&i.locked&&this.releaseLock()}))}read(t){return F(this,void 0,void 0,(function*(){if(0===t)return{done:null==this.reader,value:new Uint8Array(0)};const e=yield this.reader.read();return!e.done&&(e.value=Y(e)),e}))}}const Gn=(t,e)=>{const i=t=>n([e,t]);let n;return[e,i,new Promise((r=>(n=r)&&t.once(e,i)))]},Zn=Object.freeze({done:!0,value:void 0});class Yn{constructor(t){this._json=t}get schema(){return this._json.schema}get batches(){return this._json.batches||[]}get dictionaries(){return this._json.dictionaries||[]}}class Qn{tee(){return this._getDOMStream().tee()}pipe(t,e){return this._getNodeStream().pipe(t,e)}pipeTo(t,e){return this._getDOMStream().pipeTo(t,e)}pipeThrough(t,e){return this._getDOMStream().pipeThrough(t,e)}_getDOMStream(){return this._DOMStream||(this._DOMStream=this.toDOMStream())}_getNodeStream(){return this._nodeStream||(this._nodeStream=this.toNodeStream())}}class Xn extends Qn{constructor(){super(),this._values=[],this.resolvers=[],this._closedPromise=new Promise((t=>this._closedPromiseResolve=t))}get closed(){return this._closedPromise}cancel(t){return F(this,void 0,void 0,(function*(){yield this.return(t)}))}write(t){this._ensureOpen()&&(this.resolvers.length<=0?this._values.push(t):this.resolvers.shift().resolve({done:!1,value:t}))}abort(t){this._closedPromiseResolve&&(this.resolvers.length<=0?this._error={error:t}:this.resolvers.shift().reject({done:!0,value:t}))}close(){if(this._closedPromiseResolve){const{resolvers:t}=this;for(;t.length>0;)t.shift().resolve(Zn);this._closedPromiseResolve(),this._closedPromiseResolve=void 0}}[Symbol.asyncIterator](){return this}toDOMStream(t){return $n.toDOMStream(this._closedPromiseResolve||this._error?this:this._values,t)}toNodeStream(t){return $n.toNodeStream(this._closedPromiseResolve||this._error?this:this._values,t)}throw(t){return F(this,void 0,void 0,(function*(){return yield this.abort(t),Zn}))}return(t){return F(this,void 0,void 0,(function*(){return yield this.close(),Zn}))}read(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"read")).value}))}peek(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"peek")).value}))}next(...t){return this._values.length>0?Promise.resolve({done:!1,value:this._values.shift()}):this._error?Promise.reject({done:!0,value:this._error.error}):this._closedPromiseResolve?new Promise(((t,e)=>{this.resolvers.push({resolve:t,reject:e})})):Promise.resolve(Zn)}_ensureOpen(){if(this._closedPromiseResolve)return!0;throw new Error("AsyncQueue is closed")}}class Kn extends Xn{write(t){if((t=Y(t)).byteLength>0)return super.write(t)}toString(t=!1){return t?V(this.toUint8Array(!0)):this.toUint8Array(!1).then(V)}toUint8Array(t=!1){return t?W(this._values)[0]:(()=>F(this,void 0,void 0,(function*(){var t,e;const i=[];let n=0;try{for(var r,s=z(this);!(r=yield s.next()).done;){const t=r.value;i.push(t),n+=t.byteLength}}catch(e){t={error:e}}finally{try{r&&!r.done&&(e=s.return)&&(yield e.call(s))}finally{if(t)throw t.error}}return W(i,n)[0]})))()}}class Jn{constructor(t){t&&(this.source=new er($n.fromIterable(t)))}[Symbol.iterator](){return this}next(t){return this.source.next(t)}throw(t){return this.source.throw(t)}return(t){return this.source.return(t)}peek(t){return this.source.peek(t)}read(t){return this.source.read(t)}}class tr{constructor(t){t instanceof tr?this.source=t.source:t instanceof Kn?this.source=new ir($n.fromAsyncIterable(t)):L(t)?this.source=new ir($n.fromNodeStream(t)):R(t)?this.source=new ir($n.fromDOMStream(t)):E(t)?this.source=new ir($n.fromDOMStream(t.body)):S(t)?this.source=new ir($n.fromIterable(t)):(k(t)||C(t))&&(this.source=new ir($n.fromAsyncIterable(t)))}[Symbol.asyncIterator](){return this}next(t){return this.source.next(t)}throw(t){return this.source.throw(t)}return(t){return this.source.return(t)}get closed(){return this.source.closed}cancel(t){return this.source.cancel(t)}peek(t){return this.source.peek(t)}read(t){return this.source.read(t)}}class er{constructor(t){this.source=t}cancel(t){this.return(t)}peek(t){return this.next(t,"peek").value}read(t){return this.next(t,"read").value}next(t,e="read"){return this.source.next({cmd:e,size:t})}throw(t){return Object.create(this.source.throw&&this.source.throw(t)||Zn)}return(t){return Object.create(this.source.return&&this.source.return(t)||Zn)}}class ir{constructor(t){this.source=t,this._closedPromise=new Promise((t=>this._closedPromiseResolve=t))}cancel(t){return F(this,void 0,void 0,(function*(){yield this.return(t)}))}get closed(){return this._closedPromise}read(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"read")).value}))}peek(t){return F(this,void 0,void 0,(function*(){return(yield this.next(t,"peek")).value}))}next(t,e="read"){return F(this,void 0,void 0,(function*(){return yield this.source.next({cmd:e,size:t})}))}throw(t){return F(this,void 0,void 0,(function*(){const e=this.source.throw&&(yield this.source.throw(t))||Zn;return this._closedPromiseResolve&&this._closedPromiseResolve(),this._closedPromiseResolve=void 0,Object.create(e)}))}return(t){return F(this,void 0,void 0,(function*(){const e=this.source.return&&(yield this.source.return(t))||Zn;return this._closedPromiseResolve&&this._closedPromiseResolve(),this._closedPromiseResolve=void 0,Object.create(e)}))}}class nr extends Jn{constructor(t,e){super(),this.position=0,this.buffer=Y(t),this.size=void 0===e?this.buffer.byteLength:e}readInt32(t){const{buffer:e,byteOffset:i}=this.readAt(t,4);return new DataView(e,i).getInt32(0,!0)}seek(t){return this.position=Math.min(t,this.size),tF(this,void 0,void 0,(function*(){this.size=(yield t.stat()).size,delete this._pending})))()}readInt32(t){return F(this,void 0,void 0,(function*(){const{buffer:e,byteOffset:i}=yield this.readAt(t,4);return new DataView(e,i).getInt32(0,!0)}))}seek(t){return F(this,void 0,void 0,(function*(){return this._pending&&(yield this._pending),this.position=Math.min(t,this.size),t>>16,65535&this.buffer[1],this.buffer[0]>>>16,65535&this.buffer[0]]),i=new Uint32Array([t.buffer[1]>>>16,65535&t.buffer[1],t.buffer[0]>>>16,65535&t.buffer[0]]);let n=e[3]*i[3];this.buffer[0]=65535&n;let r=n>>>16;return n=e[2]*i[3],r+=n,n=e[3]*i[2]>>>0,r+=n,this.buffer[0]+=r<<16,this.buffer[1]=r>>>0>>16,this.buffer[1]+=e[1]*i[3]+e[2]*i[2]+e[3]*i[1],this.buffer[1]+=e[0]*i[3]+e[1]*i[2]+e[2]*i[1]+e[3]*i[0]<<16,this}_plus(t){const e=this.buffer[0]+t.buffer[0]>>>0;this.buffer[1]+=t.buffer[1],e>>0&&++this.buffer[1],this.buffer[0]=e}lessThan(t){return this.buffer[1]>>0,e[2]=this.buffer[2]+t.buffer[2]>>>0,e[1]=this.buffer[1]+t.buffer[1]>>>0,e[0]=this.buffer[0]+t.buffer[0]>>>0,e[0]>>0&&++e[1],e[1]>>0&&++e[2],e[2]>>0&&++e[3],this.buffer[3]=e[3],this.buffer[2]=e[2],this.buffer[1]=e[1],this.buffer[0]=e[0],this}hex(){return`${sr(this.buffer[3])} ${sr(this.buffer[2])} ${sr(this.buffer[1])} ${sr(this.buffer[0])}`}static multiply(t,e){return new cr(new Uint32Array(t.buffer)).times(e)}static add(t,e){return new cr(new Uint32Array(t.buffer)).plus(e)}static from(t,e=new Uint32Array(4)){return cr.fromString("string"==typeof t?t:t.toString(),e)}static fromNumber(t,e=new Uint32Array(4)){return cr.fromString(t.toString(),e)}static fromString(t,e=new Uint32Array(4)){const i=t.startsWith("-"),n=t.length,r=new cr(e);for(let e=i?1:0;e0&&this.readData(t,i)||new Uint8Array(0)}readOffsets(t,e){return this.readData(t,e)}readTypeIds(t,e){return this.readData(t,e)}readData(t,{length:e,offset:i}=this.nextBufferRange()){return this.bytes.subarray(i,i+e)}readDictionary(t){return this.dictionaries.get(t.id)}}class dr extends ur{constructor(t,e,i,n){super(new Uint8Array(0),e,i,n),this.sources=t}readNullBitmap(t,e,{offset:i}=this.nextBufferRange()){return e<=0?new Uint8Array(0):xi(this.sources[i])}readOffsets(t,{offset:e}=this.nextBufferRange()){return G(Uint8Array,G(Int32Array,this.sources[e]))}readTypeIds(t,{offset:e}=this.nextBufferRange()){return G(Uint8Array,G(t.ArrayType,this.sources[e]))}readData(t,{offset:e}=this.nextBufferRange()){const{sources:i}=this;return Et.isTimestamp(t)||(Et.isInt(t)||Et.isTime(t))&&64===t.bitWidth||Et.isDate(t)&&t.unit===s.MILLISECOND?G(Uint8Array,hr.convertArray(i[e])):Et.isDecimal(t)?G(Uint8Array,cr.convertArray(i[e])):Et.isBinary(t)||Et.isFixedSizeBinary(t)?function(t){const e=t.join(""),i=new Uint8Array(e.length/2);for(let t=0;t>1]=Number.parseInt(e.slice(t,t+2),16);return i}(i[e]):Et.isBool(t)?xi(i[e]):Et.isUtf8(t)?j(i[e].join("")):G(Uint8Array,G(t.ArrayType,i[e].map((t=>+t))))}}var fr,pr,gr,mr,br,yr,vr,wr;!function(t){t[t.BUFFER=0]="BUFFER"}(fr||(fr={})),function(t){t[t.LZ4_FRAME=0]="LZ4_FRAME",t[t.ZSTD=1]="ZSTD"}(pr||(pr={}));class _r{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsBodyCompression(t,e){return(e||new _r).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsBodyCompression(t,e){return t.setPosition(t.position()+4),(e||new _r).__init(t.readInt32(t.position())+t.position(),t)}codec(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt8(this.bb_pos+t):pr.LZ4_FRAME}method(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readInt8(this.bb_pos+t):fr.BUFFER}static startBodyCompression(t){t.startObject(2)}static addCodec(t,e){t.addFieldInt8(0,e,pr.LZ4_FRAME)}static addMethod(t,e){t.addFieldInt8(1,e,fr.BUFFER)}static endBodyCompression(t){return t.endObject()}static createBodyCompression(t,e,i){return _r.startBodyCompression(t),_r.addCodec(t,e),_r.addMethod(t,i),_r.endBodyCompression(t)}}class xr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}offset(){return this.bb.readInt64(this.bb_pos)}length(){return this.bb.readInt64(this.bb_pos+8)}static sizeOf(){return 16}static createBuffer(t,e,i){return t.prep(8,16),t.writeInt64(i),t.writeInt64(e),t.offset()}}class kr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}length(){return this.bb.readInt64(this.bb_pos)}nullCount(){return this.bb.readInt64(this.bb_pos+8)}static sizeOf(){return 16}static createFieldNode(t,e,i){return t.prep(8,16),t.writeInt64(i),t.writeInt64(e),t.offset()}}class Sr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsRecordBatch(t,e){return(e||new Sr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsRecordBatch(t,e){return t.setPosition(t.position()+4),(e||new Sr).__init(t.readInt32(t.position())+t.position(),t)}length(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt64(this.bb_pos+t):this.bb.createLong(0,0)}nodes(t,e){const i=this.bb.__offset(this.bb_pos,6);return i?(e||new kr).__init(this.bb.__vector(this.bb_pos+i)+16*t,this.bb):null}nodesLength(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.__vector_len(this.bb_pos+t):0}buffers(t,e){const i=this.bb.__offset(this.bb_pos,8);return i?(e||new xr).__init(this.bb.__vector(this.bb_pos+i)+16*t,this.bb):null}buffersLength(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.__vector_len(this.bb_pos+t):0}compression(t){const e=this.bb.__offset(this.bb_pos,10);return e?(t||new _r).__init(this.bb.__indirect(this.bb_pos+e),this.bb):null}static startRecordBatch(t){t.startObject(4)}static addLength(t,e){t.addFieldInt64(0,e,t.createLong(0,0))}static addNodes(t,e){t.addFieldOffset(1,e,0)}static startNodesVector(t,e){t.startVector(16,e,8)}static addBuffers(t,e){t.addFieldOffset(2,e,0)}static startBuffersVector(t,e){t.startVector(16,e,8)}static addCompression(t,e){t.addFieldOffset(3,e,0)}static endRecordBatch(t){return t.endObject()}}class Cr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsDictionaryBatch(t,e){return(e||new Cr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsDictionaryBatch(t,e){return t.setPosition(t.position()+4),(e||new Cr).__init(t.readInt32(t.position())+t.position(),t)}id(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt64(this.bb_pos+t):this.bb.createLong(0,0)}data(t){const e=this.bb.__offset(this.bb_pos,6);return e?(t||new Sr).__init(this.bb.__indirect(this.bb_pos+e),this.bb):null}isDelta(){const t=this.bb.__offset(this.bb_pos,8);return!!t&&!!this.bb.readInt8(this.bb_pos+t)}static startDictionaryBatch(t){t.startObject(3)}static addId(t,e){t.addFieldInt64(0,e,t.createLong(0,0))}static addData(t,e){t.addFieldOffset(1,e,0)}static addIsDelta(t,e){t.addFieldInt8(2,+e,0)}static endDictionaryBatch(t){return t.endObject()}}!function(t){t[t.HALF=0]="HALF",t[t.SINGLE=1]="SINGLE",t[t.DOUBLE=2]="DOUBLE"}(gr||(gr={}));class Ar{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFloatingPoint(t,e){return(e||new Ar).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFloatingPoint(t,e){return t.setPosition(t.position()+4),(e||new Ar).__init(t.readInt32(t.position())+t.position(),t)}precision(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):gr.HALF}static startFloatingPoint(t){t.startObject(1)}static addPrecision(t,e){t.addFieldInt16(0,e,gr.HALF)}static endFloatingPoint(t){return t.endObject()}static createFloatingPoint(t,e){return Ar.startFloatingPoint(t),Ar.addPrecision(t,e),Ar.endFloatingPoint(t)}}class Tr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsDecimal(t,e){return(e||new Tr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsDecimal(t,e){return t.setPosition(t.position()+4),(e||new Tr).__init(t.readInt32(t.position())+t.position(),t)}precision(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt32(this.bb_pos+t):0}scale(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readInt32(this.bb_pos+t):0}bitWidth(){const t=this.bb.__offset(this.bb_pos,8);return t?this.bb.readInt32(this.bb_pos+t):128}static startDecimal(t){t.startObject(3)}static addPrecision(t,e){t.addFieldInt32(0,e,0)}static addScale(t,e){t.addFieldInt32(1,e,0)}static addBitWidth(t,e){t.addFieldInt32(2,e,128)}static endDecimal(t){return t.endObject()}static createDecimal(t,e,i,n){return Tr.startDecimal(t),Tr.addPrecision(t,e),Tr.addScale(t,i),Tr.addBitWidth(t,n),Tr.endDecimal(t)}}!function(t){t[t.DAY=0]="DAY",t[t.MILLISECOND=1]="MILLISECOND"}(mr||(mr={}));class Ir{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsDate(t,e){return(e||new Ir).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsDate(t,e){return t.setPosition(t.position()+4),(e||new Ir).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):mr.MILLISECOND}static startDate(t){t.startObject(1)}static addUnit(t,e){t.addFieldInt16(0,e,mr.MILLISECOND)}static endDate(t){return t.endObject()}static createDate(t,e){return Ir.startDate(t),Ir.addUnit(t,e),Ir.endDate(t)}}!function(t){t[t.SECOND=0]="SECOND",t[t.MILLISECOND=1]="MILLISECOND",t[t.MICROSECOND=2]="MICROSECOND",t[t.NANOSECOND=3]="NANOSECOND"}(br||(br={}));class Er{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsTime(t,e){return(e||new Er).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsTime(t,e){return t.setPosition(t.position()+4),(e||new Er).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):br.MILLISECOND}bitWidth(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readInt32(this.bb_pos+t):32}static startTime(t){t.startObject(2)}static addUnit(t,e){t.addFieldInt16(0,e,br.MILLISECOND)}static addBitWidth(t,e){t.addFieldInt32(1,e,32)}static endTime(t){return t.endObject()}static createTime(t,e,i){return Er.startTime(t),Er.addUnit(t,e),Er.addBitWidth(t,i),Er.endTime(t)}}class Mr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsTimestamp(t,e){return(e||new Mr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsTimestamp(t,e){return t.setPosition(t.position()+4),(e||new Mr).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):br.SECOND}timezone(t){const e=this.bb.__offset(this.bb_pos,6);return e?this.bb.__string(this.bb_pos+e,t):null}static startTimestamp(t){t.startObject(2)}static addUnit(t,e){t.addFieldInt16(0,e,br.SECOND)}static addTimezone(t,e){t.addFieldOffset(1,e,0)}static endTimestamp(t){return t.endObject()}static createTimestamp(t,e,i){return Mr.startTimestamp(t),Mr.addUnit(t,e),Mr.addTimezone(t,i),Mr.endTimestamp(t)}}!function(t){t[t.YEAR_MONTH=0]="YEAR_MONTH",t[t.DAY_TIME=1]="DAY_TIME",t[t.MONTH_DAY_NANO=2]="MONTH_DAY_NANO"}(yr||(yr={}));class Rr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsInterval(t,e){return(e||new Rr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsInterval(t,e){return t.setPosition(t.position()+4),(e||new Rr).__init(t.readInt32(t.position())+t.position(),t)}unit(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):yr.YEAR_MONTH}static startInterval(t){t.startObject(1)}static addUnit(t,e){t.addFieldInt16(0,e,yr.YEAR_MONTH)}static endInterval(t){return t.endObject()}static createInterval(t,e){return Rr.startInterval(t),Rr.addUnit(t,e),Rr.endInterval(t)}}!function(t){t[t.Sparse=0]="Sparse",t[t.Dense=1]="Dense"}(vr||(vr={}));class Lr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsUnion(t,e){return(e||new Lr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsUnion(t,e){return t.setPosition(t.position()+4),(e||new Lr).__init(t.readInt32(t.position())+t.position(),t)}mode(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):vr.Sparse}typeIds(t){const e=this.bb.__offset(this.bb_pos,6);return e?this.bb.readInt32(this.bb.__vector(this.bb_pos+e)+4*t):0}typeIdsLength(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.__vector_len(this.bb_pos+t):0}typeIdsArray(){const t=this.bb.__offset(this.bb_pos,6);return t?new Int32Array(this.bb.bytes().buffer,this.bb.bytes().byteOffset+this.bb.__vector(this.bb_pos+t),this.bb.__vector_len(this.bb_pos+t)):null}static startUnion(t){t.startObject(2)}static addMode(t,e){t.addFieldInt16(0,e,vr.Sparse)}static addTypeIds(t,e){t.addFieldOffset(1,e,0)}static createTypeIdsVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addInt32(e[i]);return t.endVector()}static startTypeIdsVector(t,e){t.startVector(4,e,4)}static endUnion(t){return t.endObject()}static createUnion(t,e,i){return Lr.startUnion(t),Lr.addMode(t,e),Lr.addTypeIds(t,i),Lr.endUnion(t)}}class Br{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFixedSizeBinary(t,e){return(e||new Br).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFixedSizeBinary(t,e){return t.setPosition(t.position()+4),(e||new Br).__init(t.readInt32(t.position())+t.position(),t)}byteWidth(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt32(this.bb_pos+t):0}static startFixedSizeBinary(t){t.startObject(1)}static addByteWidth(t,e){t.addFieldInt32(0,e,0)}static endFixedSizeBinary(t){return t.endObject()}static createFixedSizeBinary(t,e){return Br.startFixedSizeBinary(t),Br.addByteWidth(t,e),Br.endFixedSizeBinary(t)}}class Nr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsFixedSizeList(t,e){return(e||new Nr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsFixedSizeList(t,e){return t.setPosition(t.position()+4),(e||new Nr).__init(t.readInt32(t.position())+t.position(),t)}listSize(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt32(this.bb_pos+t):0}static startFixedSizeList(t){t.startObject(1)}static addListSize(t,e){t.addFieldInt32(0,e,0)}static endFixedSizeList(t){return t.endObject()}static createFixedSizeList(t,e){return Nr.startFixedSizeList(t),Nr.addListSize(t,e),Nr.endFixedSizeList(t)}}class Fr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsMap(t,e){return(e||new Fr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsMap(t,e){return t.setPosition(t.position()+4),(e||new Fr).__init(t.readInt32(t.position())+t.position(),t)}keysSorted(){const t=this.bb.__offset(this.bb_pos,4);return!!t&&!!this.bb.readInt8(this.bb_pos+t)}static startMap(t){t.startObject(1)}static addKeysSorted(t,e){t.addFieldInt8(0,+e,0)}static endMap(t){return t.endObject()}static createMap(t,e){return Fr.startMap(t),Fr.addKeysSorted(t,e),Fr.endMap(t)}}!function(t){t[t.NONE=0]="NONE",t[t.Schema=1]="Schema",t[t.DictionaryBatch=2]="DictionaryBatch",t[t.RecordBatch=3]="RecordBatch",t[t.Tensor=4]="Tensor",t[t.SparseTensor=5]="SparseTensor"}(wr||(wr={}));class Or{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsMessage(t,e){return(e||new Or).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsMessage(t,e){return t.setPosition(t.position()+4),(e||new Or).__init(t.readInt32(t.position())+t.position(),t)}version(){const t=this.bb.__offset(this.bb_pos,4);return t?this.bb.readInt16(this.bb_pos+t):An.V1}headerType(){const t=this.bb.__offset(this.bb_pos,6);return t?this.bb.readUint8(this.bb_pos+t):wr.NONE}header(t){const e=this.bb.__offset(this.bb_pos,8);return e?this.bb.__union(t,this.bb_pos+e):null}bodyLength(){const t=this.bb.__offset(this.bb_pos,10);return t?this.bb.readInt64(this.bb_pos+t):this.bb.createLong(0,0)}customMetadata(t,e){const i=this.bb.__offset(this.bb_pos,12);return i?(e||new Ln).__init(this.bb.__indirect(this.bb.__vector(this.bb_pos+i)+4*t),this.bb):null}customMetadataLength(){const t=this.bb.__offset(this.bb_pos,12);return t?this.bb.__vector_len(this.bb_pos+t):0}static startMessage(t){t.startObject(5)}static addVersion(t,e){t.addFieldInt16(0,e,An.V1)}static addHeaderType(t,e){t.addFieldInt8(1,e,wr.NONE)}static addHeader(t,e){t.addFieldOffset(2,e,0)}static addBodyLength(t,e){t.addFieldInt64(3,e,t.createLong(0,0))}static addCustomMetadata(t,e){t.addFieldOffset(4,e,0)}static createCustomMetadataVector(t,e){t.startVector(4,e.length,4);for(let i=e.length-1;i>=0;i--)t.addOffset(e[i]);return t.endVector()}static startCustomMetadataVector(t,e){t.startVector(4,e,4)}static endMessage(t){return t.endObject()}static finishMessageBuffer(t,e){t.finish(e)}static finishSizePrefixedMessageBuffer(t,e){t.finish(e,void 0,!0)}static createMessage(t,e,i,n,r,s){return Or.startMessage(t),Or.addVersion(t,e),Or.addHeaderType(t,i),Or.addHeader(t,n),Or.addBodyLength(t,r),Or.addCustomMetadata(t,s),Or.endMessage(t)}}class Dr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsNull(t,e){return(e||new Dr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsNull(t,e){return t.setPosition(t.position()+4),(e||new Dr).__init(t.readInt32(t.position())+t.position(),t)}static startNull(t){t.startObject(0)}static endNull(t){return t.endObject()}static createNull(t){return Dr.startNull(t),Dr.endNull(t)}}class Pr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsBinary(t,e){return(e||new Pr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsBinary(t,e){return t.setPosition(t.position()+4),(e||new Pr).__init(t.readInt32(t.position())+t.position(),t)}static startBinary(t){t.startObject(0)}static endBinary(t){return t.endObject()}static createBinary(t){return Pr.startBinary(t),Pr.endBinary(t)}}class zr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsBool(t,e){return(e||new zr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsBool(t,e){return t.setPosition(t.position()+4),(e||new zr).__init(t.readInt32(t.position())+t.position(),t)}static startBool(t){t.startObject(0)}static endBool(t){return t.endObject()}static createBool(t){return zr.startBool(t),zr.endBool(t)}}class Ur{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsUtf8(t,e){return(e||new Ur).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsUtf8(t,e){return t.setPosition(t.position()+4),(e||new Ur).__init(t.readInt32(t.position())+t.position(),t)}static startUtf8(t){t.startObject(0)}static endUtf8(t){return t.endObject()}static createUtf8(t){return Ur.startUtf8(t),Ur.endUtf8(t)}}class Vr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsList(t,e){return(e||new Vr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsList(t,e){return t.setPosition(t.position()+4),(e||new Vr).__init(t.readInt32(t.position())+t.position(),t)}static startList(t){t.startObject(0)}static endList(t){return t.endObject()}static createList(t){return Vr.startList(t),Vr.endList(t)}}class Hr{constructor(){this.bb=null,this.bb_pos=0}__init(t,e){return this.bb_pos=t,this.bb=e,this}static getRootAsStruct_(t,e){return(e||new Hr).__init(t.readInt32(t.position())+t.position(),t)}static getSizePrefixedRootAsStruct_(t,e){return t.setPosition(t.position()+4),(e||new Hr).__init(t.readInt32(t.position())+t.position(),t)}static startStruct_(t){t.startObject(0)}static endStruct_(t){return t.endObject()}static createStruct_(t){return Hr.startStruct_(t),Hr.endStruct_(t)}}var jr=Sn;const $r=new class extends Kt{visit(t,e){return null==t||null==e?void 0:super.visit(t,e)}visitNull(t,e){return Dr.startNull(e),Dr.endNull(e)}visitInt(t,e){return Bn.startInt(e),Bn.addBitWidth(e,t.bitWidth),Bn.addIsSigned(e,t.isSigned),Bn.endInt(e)}visitFloat(t,e){return Ar.startFloatingPoint(e),Ar.addPrecision(e,t.precision),Ar.endFloatingPoint(e)}visitBinary(t,e){return Pr.startBinary(e),Pr.endBinary(e)}visitBool(t,e){return zr.startBool(e),zr.endBool(e)}visitUtf8(t,e){return Ur.startUtf8(e),Ur.endUtf8(e)}visitDecimal(t,e){return Tr.startDecimal(e),Tr.addScale(e,t.scale),Tr.addPrecision(e,t.precision),Tr.addBitWidth(e,t.bitWidth),Tr.endDecimal(e)}visitDate(t,e){return Ir.startDate(e),Ir.addUnit(e,t.unit),Ir.endDate(e)}visitTime(t,e){return Er.startTime(e),Er.addUnit(e,t.unit),Er.addBitWidth(e,t.bitWidth),Er.endTime(e)}visitTimestamp(t,e){const i=t.timezone&&e.createString(t.timezone)||void 0;return Mr.startTimestamp(e),Mr.addUnit(e,t.unit),void 0!==i&&Mr.addTimezone(e,i),Mr.endTimestamp(e)}visitInterval(t,e){return Rr.startInterval(e),Rr.addUnit(e,t.unit),Rr.endInterval(e)}visitList(t,e){return Vr.startList(e),Vr.endList(e)}visitStruct(t,e){return Hr.startStruct_(e),Hr.endStruct_(e)}visitUnion(t,e){Lr.startTypeIdsVector(e,t.typeIds.length);const i=Lr.createTypeIdsVector(e,t.typeIds);return Lr.startUnion(e),Lr.addMode(e,t.mode),Lr.addTypeIds(e,i),Lr.endUnion(e)}visitDictionary(t,e){const i=this.visit(t.indices,e);return Nn.startDictionaryEncoding(e),Nn.addId(e,new jr(t.id,0)),Nn.addIsOrdered(e,t.isOrdered),void 0!==i&&Nn.addIndexType(e,i),Nn.endDictionaryEncoding(e)}visitFixedSizeBinary(t,e){return Br.startFixedSizeBinary(e),Br.addByteWidth(e,t.byteWidth),Br.endFixedSizeBinary(e)}visitFixedSizeList(t,e){return Nr.startFixedSizeList(e),Nr.addListSize(e,t.listSize),Nr.endFixedSizeList(e)}visitMap(t,e){return Fr.startMap(e),Fr.addKeysSorted(e,t.keysSorted),Fr.endMap(e)}};function qr(t){return new is(t.count,Gr(t.columns),Zr(t.columns))}function Wr(t,e){return(t.children||[]).filter(Boolean).map((t=>Zi.fromJSON(t,e)))}function Gr(t){return(t||[]).reduce(((t,e)=>{return[...t,new ss(e.count,(i=e.VALIDITY,(i||[]).reduce(((t,e)=>t+ +(0===e)),0))),...Gr(e.children)];var i}),[])}function Zr(t,e=[]){for(let i=-1,n=(t||[]).length;++in),this._bodyLength="number"==typeof t?t:t.low}static fromJSON(t,i){const n=new es(0,e.V4,i);return n._createHeader=function(t,e){return()=>{switch(e){case l.Schema:return Gi.fromJSON(t);case l.RecordBatch:return is.fromJSON(t);case l.DictionaryBatch:return ns.fromJSON(t)}throw new Error(`Unrecognized Message type: { name: ${l[e]}, type: ${e} }`)}}(t,i),n}static decode(t){t=new ts(Y(t));const e=Or.getRootAsMessage(t),i=e.bodyLength(),n=e.version(),r=e.headerType(),s=new es(i,n,r);return s._createHeader=function(t,e){return()=>{switch(e){case l.Schema:return Gi.decode(t.header(new On));case l.RecordBatch:return is.decode(t.header(new Sr),t.version());case l.DictionaryBatch:return ns.decode(t.header(new Cr),t.version())}throw new Error(`Unrecognized Message type: { name: ${l[e]}, type: ${e} }`)}}(e,r),s}static encode(t){const i=new Jr;let n=-1;return t.isSchema()?n=Gi.encode(i,t.header()):t.isRecordBatch()?n=is.encode(i,t.header()):t.isDictionaryBatch()&&(n=ns.encode(i,t.header())),Or.startMessage(i),Or.addVersion(i,e.V4),Or.addHeader(i,n),Or.addHeaderType(i,t.headerType),Or.addBodyLength(i,new Kr(t.bodyLength,0)),Or.finishMessageBuffer(i,Or.endMessage(i)),i.asUint8Array()}static from(t,i=0){if(t instanceof Gi)return new es(0,e.V4,l.Schema,t);if(t instanceof is)return new es(i,e.V4,l.RecordBatch,t);if(t instanceof ns)return new es(i,e.V4,l.DictionaryBatch,t);throw new Error(`Unrecognized Message header: ${t}`)}get type(){return this.headerType}get version(){return this._version}get headerType(){return this._headerType}get bodyLength(){return this._bodyLength}header(){return this._createHeader()}isSchema(){return this.headerType===l.Schema}isRecordBatch(){return this.headerType===l.RecordBatch}isDictionaryBatch(){return this.headerType===l.DictionaryBatch}}class is{constructor(t,e,i){this._nodes=e,this._buffers=i,this._length="number"==typeof t?t:t.low}get nodes(){return this._nodes}get length(){return this._length}get buffers(){return this._buffers}}class ns{constructor(t,e,i=!1){this._data=t,this._isDelta=i,this._id="number"==typeof e?e:e.low}get id(){return this._id}get data(){return this._data}get isDelta(){return this._isDelta}get length(){return this.data.length}get nodes(){return this.data.nodes}get buffers(){return this.data.buffers}}class rs{constructor(t,e){this.offset="number"==typeof t?t:t.low,this.length="number"==typeof e?e:e.low}}class ss{constructor(t,e){this.length="number"==typeof t?t:t.low,this.nullCount="number"==typeof e?e:e.low}}function os(t,e){const i=[];for(let n,r=-1,s=-1,o=t.childrenLength();++rZi.encode(t,e))),l=Fn.createChildrenVector(t,a),h=e.metadata&&e.metadata.size>0?Fn.createCustomMetadataVector(t,[...e.metadata].map((([e,i])=>{const n=t.createString(`${e}`),r=t.createString(`${i}`);return Ln.startKeyValue(t),Ln.addKey(t,n),Ln.addValue(t,r),Ln.endKeyValue(t)}))):-1;return e.name&&(i=t.createString(e.name)),Fn.startField(t),Fn.addType(t,n),Fn.addTypeType(t,o),Fn.addChildren(t,l),Fn.addNullable(t,!!e.nullable),-1!==i&&Fn.addName(t,i),-1!==r&&Fn.addDictionary(t,r),-1!==h&&Fn.addCustomMetadata(t,h),Fn.endField(t)},Zi.decode=function(t,e){let i,n,r,s,o,a;return e&&(a=t.dictionary())?e.has(i=a.id().low)?(s=(s=a.indexType())?ls(s):new Lt,o=new Qt(e.get(i),s,i,a.isOrdered()),n=new Zi(t.name(),o,t.nullable(),as(t))):(s=(s=a.indexType())?ls(s):new Lt,e.set(i,r=hs(t,os(t,e))),o=new Qt(r,s,i,a.isOrdered()),n=new Zi(t.name(),o,t.nullable(),as(t))):(r=hs(t,os(t,e)),n=new Zi(t.name(),r,t.nullable(),as(t))),n||null},Zi.fromJSON=function(t,e){let i,n,r,s,o,a;return e&&(s=t.dictionary)?e.has(i=s.id)?(n=(n=s.indexType)?Qr(n):new Lt,a=new Qt(e.get(i),n,i,s.isOrdered),r=new Zi(t.name,a,t.nullable,Yr(t.customMetadata))):(n=(n=s.indexType)?Qr(n):new Lt,e.set(i,o=Xr(t,Wr(t,e))),a=new Qt(o,n,i,s.isOrdered),r=new Zi(t.name,a,t.nullable,Yr(t.customMetadata))):(o=Xr(t,Wr(t,e)),r=new Zi(t.name,o,t.nullable,Yr(t.customMetadata))),r||null},Gi.encode=function(t,e){const i=e.fields.map((e=>Zi.encode(t,e)));On.startFieldsVector(t,i.length);const n=On.createFieldsVector(t,i),r=e.metadata&&e.metadata.size>0?On.createCustomMetadataVector(t,[...e.metadata].map((([e,i])=>{const n=t.createString(`${e}`),r=t.createString(`${i}`);return Ln.startKeyValue(t),Ln.addKey(t,n),Ln.addValue(t,r),Ln.endKeyValue(t)}))):-1;return On.startSchema(t),On.addFields(t,n),On.addEndianness(t,cs?Tn.Little:Tn.Big),-1!==r&&On.addCustomMetadata(t,r),On.endSchema(t)},Gi.decode=function(t,e=new Map){const i=function(t,e){const i=[];for(let n,r=-1,s=-1,o=t.fieldsLength();++rZi.fromJSON(t,e)))}(t,e),Yr(t.customMetadata),e)},is.encode=function(t,e){const i=e.nodes||[],n=e.buffers||[];Sr.startNodesVector(t,i.length);for(const e of i.slice().reverse())ss.encode(t,e);const r=t.endVector();Sr.startBuffersVector(t,n.length);for(const e of n.slice().reverse())rs.encode(t,e);const s=t.endVector();return Sr.startRecordBatch(t),Sr.addLength(t,new Kr(e.length,0)),Sr.addNodes(t,r),Sr.addBuffers(t,s),Sr.endRecordBatch(t)},is.decode=function(t,i=e.V4){if(null!==t.compression())throw new Error("Record batch compression not implemented");return new is(t.length(),function(t){const e=[];for(let i,n=-1,r=-1,s=t.nodesLength();++n{const t=new ArrayBuffer(2);return new DataView(t).setInt16(0,256,!0),256===new Int16Array(t)[0]})(),us=t=>`Expected ${l[t]} Message in stream, but was null or length 0.`,ds=t=>`Header pointer of flatbuffer-encoded ${l[t]} Message is null or length 0.`,fs=(t,e)=>`Expected to read ${t} metadata bytes, but only read ${e}.`,ps=(t,e)=>`Expected to read ${t} bytes for message body, but only read ${e}.`;class gs{constructor(t){this.source=t instanceof Jn?t:new Jn(t)}[Symbol.iterator](){return this}next(){let t;return(t=this.readMetadataLength()).done||-1===t.value&&(t=this.readMetadataLength()).done||(t=this.readMetadata(t.value)).done?Zn:t}throw(t){return this.source.throw(t)}return(t){return this.source.return(t)}readMessage(t){let e;if((e=this.next()).done)return null;if(null!=t&&e.value.headerType!==t)throw new Error(us(t));return e.value}readMessageBody(t){if(t<=0)return new Uint8Array(0);const e=Y(this.source.read(t));if(e.byteLength[...e,...i.VALIDITY&&[i.VALIDITY]||[],...i.TYPE&&[i.TYPE]||[],...i.OFFSET&&[i.OFFSET]||[],...i.DATA&&[i.DATA]||[],...t(i.children)]),[])}(this._body)}readMessage(t){let e;if((e=this.next()).done)return null;if(null!=t&&e.value.headerType!==t)throw new Error(us(t));return e.value}readSchema(){const t=l.Schema,e=this.readMessage(t),i=null==e?void 0:e.header();if(!e||!i)throw new Error(ds(t));return i}}const ys=4,vs=new Uint8Array(6);for(let t=0;t<6;t+=1)vs[t]="ARROW1".codePointAt(t);function ws(t,e=0){for(let i=-1,n=vs.length;++ithis)):this}readRecordBatch(t){return this._impl.isFile()?this._impl.readRecordBatch(t):null}[Symbol.iterator](){return this._impl[Symbol.iterator]()}[Symbol.asyncIterator](){return this._impl[Symbol.asyncIterator]()}toDOMStream(){return $n.toDOMStream(this.isSync()?{[Symbol.iterator]:()=>this}:{[Symbol.asyncIterator]:()=>this})}toNodeStream(){return $n.toNodeStream(this.isSync()?{[Symbol.iterator]:()=>this}:{[Symbol.asyncIterator]:()=>this},{objectMode:!0})}static throughNode(t){throw new Error('"throughNode" not available in this environment')}static throughDOM(t,e){throw new Error('"throughDOM" not available in this environment')}static from(t){return t instanceof Ss?t:A(t)?function(t){return new Cs(new Ns(t))}(t):I(t)?function(t){return F(this,void 0,void 0,(function*(){const{size:e}=yield t.stat(),i=new rr(t,e);return e>=ks&&ws(yield i.readAt(0,_s+7&-8))?new Is(new Bs(i)):new As(new Rs(i))}))}(t):k(t)?(()=>F(this,void 0,void 0,(function*(){return yield Ss.from(yield t)})))():E(t)||R(t)||L(t)||C(t)?function(t){return F(this,void 0,void 0,(function*(){const e=yield t.peek(_s+7&-8);return e&&e.byteLength>=4?ws(e)?new Ts(new Ls(yield t.read())):new As(new Rs(t)):new As(new Rs(function(){return D(this,arguments,(function*(){}))}()))}))}(new tr(t)):function(t){const e=t.peek(_s+7&-8);return e&&e.byteLength>=4?ws(e)?new Ts(new Ls(t.read())):new Cs(new Ms(t)):new Cs(new Ms(function*(){}()))}(new Jn(t))}static readAll(t){return t instanceof Ss?t.isSync()?Os(t):Ds(t):A(t)||ArrayBuffer.isView(t)||S(t)||T(t)?Os(t):Ds(t)}}class Cs extends Ss{constructor(t){super(t),this._impl=t}readAll(){return[...this]}[Symbol.iterator](){return this._impl[Symbol.iterator]()}[Symbol.asyncIterator](){return D(this,arguments,(function*(){yield O(yield*P(z(this[Symbol.iterator]())))}))}}class As extends Ss{constructor(t){super(t),this._impl=t}readAll(){var t,e;return F(this,void 0,void 0,(function*(){const i=new Array;try{for(var n,r=z(this);!(n=yield r.next()).done;){const t=n.value;i.push(t)}}catch(e){t={error:e}}finally{try{n&&!n.done&&(e=r.return)&&(yield e.call(r))}finally{if(t)throw t.error}}return i}))}[Symbol.iterator](){throw new Error("AsyncRecordBatchStreamReader is not Iterable")}[Symbol.asyncIterator](){return this._impl[Symbol.asyncIterator]()}}class Ts extends Cs{constructor(t){super(t),this._impl=t}}class Is extends As{constructor(t){super(t),this._impl=t}}class Es{constructor(t=new Map){this.closed=!1,this.autoDestroy=!0,this._dictionaryIndex=0,this._recordBatchIndex=0,this.dictionaries=t}get numDictionaries(){return this._dictionaryIndex}get numRecordBatches(){return this._recordBatchIndex}isSync(){return!1}isAsync(){return!1}isFile(){return!1}isStream(){return!1}reset(t){return this._dictionaryIndex=0,this._recordBatchIndex=0,this.schema=t,this.dictionaries=new Map,this}_loadRecordBatch(t,e){const i=this._loadVectors(t,e,this.schema.fields),n=Wi({type:new jt(this.schema.fields),length:t.length,children:i});return new dn(this.schema,n)}_loadDictionaryBatch(t,e){const{id:i,isDelta:n}=t,{dictionaries:r,schema:s}=this,o=r.get(i);if(n||!o){const r=s.dictionaries.get(i),a=this._loadVectors(t.data,e,[r]);return(o&&n?o.concat(new Hi(a)):new Hi(a)).memoize()}return o.memoize()}_loadVectors(t,e,i){return new ur(e,t.nodes,t.buffers,this.dictionaries).visitMany(i)}}class Ms extends Es{constructor(t,e){super(e),this._reader=A(t)?new bs(this._handle=t):new gs(this._handle=t)}isSync(){return!0}isStream(){return!0}[Symbol.iterator](){return this}cancel(){!this.closed&&(this.closed=!0)&&(this.reset()._reader.return(),this._reader=null,this.dictionaries=null)}open(t){return 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i)this.popoverContent.appendChild(t.object);Di(t,this.popover,this.popoverContent)}hide(){this.popover.style.display="none",this.dispose()}dispose(){this.popover&&this.popover.parentNode.removeChild(this.popover);const t=Object.keys(this);for(let e of t)this[e]=void 0}}function Di(t,e,i){const{x:n,y:r,width:s}=we(t,e.parentNode);e.style.top=`${r}px`;const{width:o}=e.getBoundingClientRect(),a=n+o,l=a-s;e.style.left=`${a>s?n-l:n}px`,i.style.maxWidth=`${Math.min(o,s)}px`}class Pi extends Li{constructor({parent:t,width:e}){super({parent:t,width:e,border:"1px solid gray"})}configure(t,e){this.colorHandlers=e,this.setActiveColorHandler("color"),this.createSwatches(t)}setActiveColorHandler(t){this.activeColorHandler=this.colorHandlers[t]}createSwatches(t){this.container.querySelectorAll(".igv-ui-color-swatch").forEach((t=>t.remove()));const e=Object.values(Ri);for(let t of e){const e=pe({class:"igv-ui-color-swatch"});this.container.appendChild(e),this.decorateSwatch(e,t)}if(t)for(let e of t){const t=pe({class:"igv-ui-color-swatch"});this.container.appendChild(t),this.decorateSwatch(t,e)}}decorateSwatch(t,e){t.style.backgroundColor=e,t.addEventListener("mouseenter",(()=>t.style.borderColor=e)),t.addEventListener("mouseleave",(()=>t.style.borderColor="white")),t.addEventListener("click",(t=>{t.stopPropagation(),this.activeColorHandler(e)})),t.addEventListener("touchend",(t=>{t.stopPropagation(),this.activeColorHandler(e)}))}}if("undefined"!=typeof document){function py(t){for(let e of document.styleSheets)if(e=e.href?e.href.replace(/^.*[\\\/]/,""):"",e===t)return!0;return!1}py("igv-ui.css")||function(){const t=document.createElement("style");t.setAttribute("type","text/css"),t.setAttribute("title","igv-ui.css"),t.innerHTML='.igv-ui-popover {\n cursor: default;\n position: absolute;\n z-index: 2048;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: 1px;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n background-color: white;\n}\n.igv-ui-popover > div:first-child {\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-popover > div:first-child > div:first-child {\n margin-left: 4px;\n}\n.igv-ui-popover > div:first-child > div:last-child {\n margin-right: 4px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-ui-popover > div:first-child > div:last-child:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-ui-popover > div:last-child {\n overflow-y: auto;\n overflow-x: hidden;\n max-height: 400px;\n max-width: 800px;\n background-color: white;\n}\n.igv-ui-popover > div:last-child > div {\n user-select: all;\n margin-left: 4px;\n margin-right: 4px;\n min-width: 220px;\n overflow-x: hidden;\n text-overflow: ellipsis;\n white-space: nowrap;\n}\n.igv-ui-popover > div:last-child > div > span {\n font-weight: bolder;\n}\n.igv-ui-popover > div:last-child hr {\n width: 100%;\n}\n\n.igv-ui-alert-dialog-container {\n box-sizing: content-box;\n position: absolute;\n z-index: 2048;\n top: 50%;\n left: 50%;\n width: 400px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n outline: none;\n font-family: "Open Sans", sans-serif;\n font-size: 15px;\n font-weight: 400;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n}\n.igv-ui-alert-dialog-container > div:first-child {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-alert-dialog-container > div:first-child div:first-child {\n padding-left: 8px;\n}\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body {\n -webkit-user-select: text;\n -moz-user-select: text;\n -ms-user-select: text;\n user-select: text;\n color: #373737;\n width: 100%;\n height: calc(100% - 24px - 64px);\n overflow-y: scroll;\n}\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body .igv-ui-alert-dialog-body-copy {\n margin: 16px;\n width: auto;\n height: auto;\n overflow-wrap: break-word;\n word-break: break-word;\n background-color: white;\n border: unset;\n}\n.igv-ui-alert-dialog-container > div:last-child {\n width: 100%;\n margin-bottom: 10px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n}\n.igv-ui-alert-dialog-container > div:last-child div {\n margin: unset;\n width: 40px;\n height: 30px;\n line-height: 30px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n border-color: #2B81AF;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-ui-alert-dialog-container > div:last-child div:hover {\n cursor: pointer;\n border-color: #25597f;\n background-color: #25597f;\n}\n\n.igv-ui-color-swatch {\n position: relative;\n box-sizing: content-box;\n display: flex;\n flex-flow: row;\n flex-wrap: wrap;\n justify-content: center;\n align-items: center;\n width: 32px;\n height: 32px;\n border-style: solid;\n border-width: 2px;\n border-color: white;\n border-radius: 4px;\n}\n\n.igv-ui-color-swatch:hover {\n border-color: dimgray;\n}\n\n.igv-ui-colorpicker-menu-close-button {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 32px;\n margin-top: 4px;\n margin-bottom: 4px;\n padding-right: 8px;\n}\n.igv-ui-colorpicker-menu-close-button i.fa {\n display: block;\n margin-left: 4px;\n margin-right: 4px;\n color: #5f5f5f;\n}\n.igv-ui-colorpicker-menu-close-button i.fa:hover,\n.igv-ui-colorpicker-menu-close-button i.fa:focus,\n.igv-ui-colorpicker-menu-close-button i.fa:active {\n cursor: pointer;\n color: #0f0f0f;\n}\n\n.igv-ui-generic-dialog-container {\n box-sizing: content-box;\n position: fixed;\n top: 0;\n left: 0;\n width: 300px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n z-index: 2048;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-one-liner {\n color: #373737;\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin-top: 8px;\n padding-left: 8px;\n overflow-wrap: break-word;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input {\n margin-top: 8px;\n width: 95%;\n height: 24px;\n color: #373737;\n line-height: 24px;\n padding-left: 8px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input div {\n width: 30%;\n height: 100%;\n font-size: 16px;\n text-align: right;\n padding-right: 8px;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\n width: 50%;\n font-size: 16px;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input {\n margin-top: 8px;\n width: calc(100% - 16px);\n height: 24px;\n color: #373737;\n line-height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\n font-size: 16px;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel {\n width: 100%;\n height: 28px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div {\n margin-top: 32px;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:first-child {\n margin-left: 32px;\n margin-right: 0;\n background-color: #5ea4e0;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:last-child {\n margin-left: 0;\n margin-right: 32px;\n background-color: #c4c4c4;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f;\n}\n\n.igv-ui-generic-container {\n box-sizing: content-box;\n position: absolute;\n z-index: 2048;\n background-color: white;\n cursor: pointer;\n display: flex;\n flex-direction: row;\n flex-wrap: wrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ui-generic-container > div:first-child {\n cursor: move;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n height: 24px;\n width: 100%;\n background-color: #dddddd;\n}\n.igv-ui-generic-container > div:first-child > div {\n display: block;\n color: #5f5f5f;\n cursor: pointer;\n width: 14px;\n height: 14px;\n margin-right: 8px;\n margin-bottom: 4px;\n}\n\n.igv-ui-dialog {\n z-index: 2048;\n position: fixed;\n width: fit-content;\n height: fit-content;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n background-color: white;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n}\n.igv-ui-dialog .igv-ui-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-ui-dialog .igv-ui-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-ui-dialog .igv-ui-dialog-header div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-ui-dialog .igv-ui-dialog-one-liner {\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin: 8px;\n overflow-wrap: break-word;\n background-color: white;\n font-weight: bold;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel {\n width: 100%;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div {\n margin: 16px;\n margin-top: 32px;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child {\n background-color: #5ea4e0;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child {\n background-color: #c4c4c4;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f;\n}\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f;\n}\n.igv-ui-dialog .igv-ui-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-ui-dialog .igv-ui-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-ui-dialog .igv-ui-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f;\n}\n\n.igv-ui-panel, .igv-ui-panel-row, .igv-ui-panel-column {\n z-index: 2048;\n background-color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n display: flex;\n justify-content: flex-start;\n align-items: flex-start;\n}\n\n.igv-ui-panel-column {\n display: flex;\n flex-direction: column;\n}\n\n.igv-ui-panel-row {\n display: flex;\n flex-direction: row;\n}\n\n.igv-ui-textbox {\n background-color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n display: flex;\n justify-content: flex-start;\n align-items: flex-start;\n}\n\n.igv-ui-table {\n background-color: white;\n}\n\n.igv-ui-table thead {\n position: sticky;\n top: 0;\n}\n\n.igv-ui-table th {\n text-align: left;\n}\n\n.igv-ui-table td {\n padding-right: 20px;\n}\n\n.igv-ui-table tr:hover {\n background-color: lightblue;\n}\n\n/*# sourceMappingURL=igv-ui.css.map */\n',document.head.append(t)}()}function zi(t,e){const i=_e.div({class:"igv-menu-popup-check-container"}),n=_e.div();i.appendChild(n);const r=_i.createIcon("check",!0===e?"#444":"transparent");n.appendChild(r);const s=_e.div();return s.innerText=t,i.appendChild(s),i}const Ui={trackMenuItemList:function(t){const e=new Set(["alignment","annotation","variant","eqtl","snp"]),i=t.track.config&&void 0!==t.track.config.visibilityWindow;let n=[];return"sequence"!==t.track.config.type&&(n.push(function(t){const e=fe("
");return e.text("Set track name"),{object:e,click:e=>{const i={label:"Track Name",value:(n=t.track,n.trackView.viewports[0].$trackLabel.text()||"unnamed"),callback:function(){let e=t.browser.inputDialog.value;e=""===e||void 0===e?"untitled":e.trim(),t.track.name=e}};var n;t.browser.inputDialog.present(i,e)}}}(t)),n.push(function(t){const e=fe("
");return e.text("Set track height"),{object:e,click:e=>{const i={label:"Track Height",value:t.track.height,callback:()=>{const e=Number(t.browser.inputDialog.value,10);void 0!==e&&(void 0!==t.track.minHeight&&t.track.minHeight>e&&(t.track.minHeight=e),void 0!==t.track.maxHeight&&t.track.maxHeight"),n.push(Vi({trackView:t,label:"Set track color",option:"color"})),n.push(function({trackView:t,label:e}){const i=fe("
");return i.text(e),{object:i,click:()=>{t.track.color=void 0,t.repaintViews()}}}({trackView:t,label:"Unset track color"})),"wig"!==t.track.config.type&&"annotation"!==t.track.config.type||(n.push(Vi({trackView:t,label:"Set alt color",option:"altColor"})),n.push(function({trackView:t,label:e}){const i=fe("
");return i.text(e),{object:i,click:()=>{t.track.altColor=void 0,t.repaintViews()}}}({trackView:t,label:"Unset alt color"})))),t.track.menuItemList&&(n=n.concat(t.track.menuItemList())),(i||e.has(t.track.type))&&(n.push("
"),n.push(function(t){const e=fe("
");return e.text("Set visibility window"),{object:e,click:e=>{const i={label:"Visibility Window",value:t.track.visibilityWindow,callback:()=>{let e=t.browser.inputDialog.value;e=""===e||void 0===e?-1:e.trim(),t.track.visibilityWindow=Number.parseInt(e),t.track.config.visibilityWindow=Number.parseInt(e),t.updateViews()}};t.browser.inputDialog.present(i,e)}}}(t))),!1!==t.track.removable&&(n.push("
"),n.push(function(t){const e=fe("
");return e.text("Remove track"),{object:e,click:()=>t.browser.removeTrack(t.track)}}(t))),n},numericDataMenuItems:function(t){const e=[];e.push("
");const i=fe("
");return i.text("Set data range"),e.push({object:i,click:()=>{t.browser.dataRangeDialog.configure(t),t.browser.dataRangeDialog.present(fe(t.browser.columnContainer))}}),void 0!==t.track.logScale&&e.push({object:fe(zi("Log scale",t.track.logScale)),click:()=>{t.track.logScale=!t.track.logScale,t.repaintViews()}}),e.push({object:fe(zi("Autoscale",t.track.autoscale)),click:()=>{t.track.autoscale=!t.track.autoscale,t.updateViews()}}),e},trackMenuItemListHelper:function(t,e){var i=[];return t.length>0&&(i=t.map((function(t,i){var n;if(t.name?(n=fe("
")).text(t.name):t.object?n=t.object:"string"==typeof t.label?(n=fe("
")).html(t.label):"string"==typeof t&&(n=t.startsWith("<")?fe(t):fe("
"+t+"
")),0===i&&n.addClass("igv-track-menu-border-top"),t.click){function r(i){t.click(i),e.hide(),i.preventDefault(),i.stopPropagation()}n.on("click",r),n.on("touchend",(function(t){r(t)})),n.on("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}return{object:n,init:t.init||void 0}}))),i},showColorPicker:t=>void 0===t.type||"bedtype"===t.type||"alignment"===t.type||"annotation"===t.type||"variant"===t.type||"wig"===t.type||"interact"===t.type,createMenuItem(t,e){const i=fe("
");return i.text(t),{object:i,click:e}}};function Vi({trackView:t,label:e,option:i}){const n=fe("
");return n.text(e),{object:n,click:()=>t.presentColorPicker(i)}}class Hi{constructor(t,e,i){this.browser=t,this.$container=fe("
",{class:"igv-generic-dialog-container"}),e.append(this.$container),this.$container.offset({left:0,top:0});const n=fe("
",{class:"igv-generic-dialog-header"});this.$container.append(n),ki.attachDialogCloseHandlerWithParent(n[0],(()=>{this.$minimum_input.val(void 0),this.$maximum_input.val(void 0),this.$container.offset({left:0,top:0}),this.$container.hide()})),this.$minimum=fe("
",{class:"igv-generic-dialog-label-input"}),this.$container.append(this.$minimum);const r=fe("
");r.text("Minimum"),this.$minimum.append(r),this.$minimum_input=fe(""),this.$minimum.append(this.$minimum_input),this.$maximum=fe("
",{class:"igv-generic-dialog-label-input"}),this.$container.append(this.$maximum);const s=fe("
");s.text("Maximum"),this.$maximum.append(s),this.$maximum_input=fe(""),this.$maximum.append(this.$maximum_input);const o=fe("
",{class:"igv-generic-dialog-ok-cancel"});this.$container.append(o),this.$ok=fe("
"),o.append(this.$ok),this.$ok.text("OK"),this.$cancel=fe("
"),o.append(this.$cancel),this.$cancel.text("Cancel"),this.$cancel.on("click",(()=>{this.$minimum_input.val(void 0),this.$maximum_input.val(void 0),this.$container.offset({left:0,top:0}),this.$container.hide()})),Ci(this.$container.get(0),n.get(0)),this.$container.hide()}configure(t){const e=t.dataRange();let i,n;e?(i=e.min,n=e.max):(i=0,n=100),this.$minimum_input.val(i),this.$maximum_input.val(n),this.$minimum_input.unbind(),this.$minimum_input.on("keyup",(e=>{13===e.keyCode&&this.processResults(t)})),this.$maximum_input.unbind(),this.$maximum_input.on("keyup",(e=>{13===e.keyCode&&this.processResults(t)})),this.$ok.unbind(),this.$ok.on("click",(e=>{this.processResults(t)}))}processResults(t){const e=Number(this.$minimum_input.val()),i=Number(this.$maximum_input.val());isNaN(e)||isNaN(i)?this.browser.alert.present(new Error("Must input numeric values"),void 0):t.setDataRange(e,i),this.$minimum_input.val(void 0),this.$maximum_input.val(void 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i,n,r;for(;;){if(t.lookahead=3&&(t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart),t.prev_length=t.match_length,t.prev_match=t.match_start,t.match_length=2,0!==i&&t.prev_length4096)&&(t.match_length=2)),t.prev_length>=3&&t.match_length<=t.prev_length){r=t.strstart+t.lookahead-3,n=Vn(t,t.strstart-1-t.prev_match,t.prev_length-3),t.lookahead-=t.prev_length-1,t.prev_length-=2;do{++t.strstart<=r&&(t.ins_h=mr(t,t.ins_h,t.window[t.strstart+3-1]),i=t.prev[t.strstart&t.w_mask]=t.head[t.ins_h],t.head[t.ins_h]=t.strstart)}while(0!=--t.prev_length);if(t.match_available=0,t.match_length=2,t.strstart++,n&&(yr(t,!1),0===t.strm.avail_out))return 1}else if(t.match_available){if(n=Vn(t,0,t.window[t.strstart-1]),n&&yr(t,!1),t.strstart++,t.lookahead--,0===t.strm.avail_out)return 1}else t.match_available=1,t.strstart++,t.lookahead--}return t.match_available&&(n=Vn(t,0,t.window[t.strstart-1]),t.match_available=0),t.insert=t.strstart<2?t.strstart:2,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2};function Tr(t,e,i,n,r){this.good_length=t,this.max_lazy=e,this.nice_length=i,this.max_chain=n,this.func=r}const Ir=[new Tr(0,0,0,0,Sr),new Tr(4,4,8,4,Cr),new Tr(4,5,16,8,Cr),new Tr(4,6,32,32,Cr),new Tr(4,4,16,16,Ar),new Tr(8,16,32,32,Ar),new Tr(8,16,128,128,Ar),new Tr(8,32,128,256,Ar),new Tr(32,128,258,1024,Ar),new Tr(32,258,258,4096,Ar)];function Er(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=or,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(1146),this.dyn_dtree=new Uint16Array(122),this.bl_tree=new Uint16Array(78),pr(this.dyn_ltree),pr(this.dyn_dtree),pr(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(16),this.heap=new Uint16Array(573),pr(this.heap),this.heap_len=0,this.heap_max=0,this.depth=new 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e===Zn&&((i=t.state).window_size=2*i.w_size,pr(i.head),i.max_lazy_match=Ir[i.level].max_lazy,i.good_match=Ir[i.level].good_length,i.nice_match=Ir[i.level].nice_length,i.max_chain_length=Ir[i.level].max_chain,i.strstart=0,i.block_start=0,i.lookahead=0,i.insert=0,i.match_length=i.prev_length=2,i.match_available=0,i.ins_h=0),e},Br=(t,e,i,n,r,s)=>{if(!t)return Qn;let o=1;if(e===Jn&&(e=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||i!==or||n<8||n>15||e<0||e>9||s<0||s>nr||8===n&&1!==o)return dr(t,Qn);8===n&&(n=9);const a=new Er;return t.state=a,a.strm=t,a.status=hr,a.wrap=o,a.gzhead=null,a.w_bits=n,a.w_size=1<Br(t,e,or,15,8,rr),deflateInit2:Br,deflateReset:Lr,deflateResetKeep:Rr,deflateSetHeader:(t,e)=>Mr(t)||2!==t.state.wrap?Qn:(t.state.gzhead=e,Zn),deflate:(t,e)=>{if(Mr(t)||e>Gn||e<0)return t?dr(t,Qn):Qn;const i=t.state;if(!t.output||0!==t.avail_in&&!t.input||i.status===ur&&e!==Wn)return dr(t,0===t.avail_out?Kn:Qn);const 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o=t.window;for(;;){if(t.lookahead<=ar){if(kr(t),t.lookahead<=ar&&e===jn)return 1;if(0===t.lookahead)break}if(t.match_length=0,t.lookahead>=3&&t.strstart>0&&(r=t.strstart-1,n=o[r],n===o[++r]&&n===o[++r]&&n===o[++r])){s=t.strstart+ar;do{}while(n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&n===o[++r]&&rt.lookahead&&(t.match_length=t.lookahead)}if(t.match_length>=3?(i=Vn(t,1,t.match_length-3),t.lookahead-=t.match_length,t.strstart+=t.match_length,t.match_length=0):(i=Vn(t,0,t.window[t.strstart]),t.lookahead--,t.strstart++),i&&(yr(t,!1),0===t.strm.avail_out))return 1}return t.insert=0,e===Wn?(yr(t,!0),0===t.strm.avail_out?3:4):t.sym_next&&(yr(t,!1),0===t.strm.avail_out)?1:2})(i,e):Ir[i.level].func(i,e);if(3!==n&&4!==n||(i.status=ur),1===n||3===n)return 0===t.avail_out&&(i.last_flush=-1),Zn;if(2===n&&(e===$n?Hn(i):e!==Gn&&(zn(i,0,0,!1),e===qn&&(pr(i.head),0===i.lookahead&&(i.strstart=0,i.block_start=0,i.insert=0))),br(t),0===t.avail_out))return 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this.offset+this.sequence.length}}const Da=function(t,e,i,n){this.chr=t,this.start=e,this.end=i,this.features=n};Da.prototype.contains=function(t,e,i){return this.chr===t&&this.start<=e&&this.end>=i},Da.prototype.containsRange=function(t){return this.chr===t.chr&&this.start<=t.start&&this.end>=t.end};const Pa=qi,za=new Set(["fastaURL","indexURL","compressedIndexURL","cytobandURL","indexed"]);class Ua{constructor(t){this.file=t.fastaURL,this.indexFile=t.indexURL||t.indexFile||this.file+".fai",this.compressedIndexFile=t.compressedIndexURL||!1,this.withCredentials=t.withCredentials,this.chromosomeNames=[],this.chromosomes={},this.sequences={},this.offsets={};const e={};for(let i in t)t.hasOwnProperty(i)&&!za.has(i)&&(e[i]=t[i]);this.config=e}async init(){return this.getIndex()}async getSequence(t,e,i){if(!this.interval||!this.interval.contains(t,e,i)){let n=e,r=i;if(i-e<5e4){const t=i-e,s=Math.round(e+t/2);n=Math.max(0,s-25e3),r=s+25e3}const s=await this.readSequence(t,n,r);this.interval=new Da(t,n,r,s)}const n=e-this.interval.start,r=i-e;return this.interval.features?this.interval.features.substr(n,r):null}async getIndex(){if(this.index)return this.index;{const t=await zo.load(this.indexFile,la(this.config)),e=Pa(t),i=e.length;let n=0,r=0;for(this.index={};nthis.compressedIndex[n][1])return[n];let r=0,s=n,o=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,l=!1;for(let e=0;et){l=!0;break}e=e));t++);const h=i[i.length-1];return h===this.compressedIndex.length-1&&this.compressedIndex[h][1]0&&(b=Math.min(s-r,a-d),y+=m.substr(v,b),v+=b+h);v{this.reversed=!this.reversed,this.trackView.repaintViews()}},{name:this.frameTranslate?"Close Translation":"Three-frame Translate",click:()=>{if(this.frameTranslate=!this.frameTranslate,this.frameTranslate){for(let t of this.trackView.viewports)t.setContentHeight(Qa);this.trackView.setTrackHeight(Qa)}else{for(let t of this.trackView.viewports)t.setContentHeight(25);this.trackView.setTrackHeight(25)}this.trackView.repaintViews()}}]}contextMenuItemList(t){const e=t.viewport;if(e.referenceFrame.bpPerPixel<=1){const t=e.getWidth()*e.referenceFrame.bpPerPixel,i=e.referenceFrame.chr,n=Math.floor(e.referenceFrame.start),r=Math.ceil(n+t),s=[{label:this.reversed?"View visible sequence (reversed)...":"View visible sequence...",click:async()=>{let t=await this.browser.genome.sequence.getSequence(i,n,r);t?this.reversed&&(t=Ra(t)):t="Unknown sequence",this.browser.alert.present(t)}}];return ba()&&s.push({label:"Copy visible sequence",click:async()=>{let t=await this.browser.genome.sequence.getSequence(i,n,r);t?this.reversed&&(t=Ra(t)):t="Unknown sequence";try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),s.push("
"),s}}translateSequence(t){const e=[[],[],[]];for(let i of[0,1,2]){let n=i;for(;t.length-n>=3;){let r=t.slice(n,n+3);this.reversed&&(r=r.split("").reverse().join(""));const s=Wa[r.toUpperCase()]||"";e[i].push({codons:r,aminoA:s}),n+=3}}return e}async getSequenceSource(){return this.config.fastaURL?(this.fasta||(this.fasta=new Ka(this.config,this.browser.genome),await this.fasta.init()),this.fasta):this.browser.genome.sequence}async getFeatures(t,e,i,n){if(e=Math.floor(e),i=Math.floor(i),n&&n>10)return null;{const n=await this.getSequenceSource();return{bpStart:e,sequence:await n.getSequence(t,e,i)}}}draw(t){const e=t.context;if(t.features){let i=t.features.sequence;if(!i)return;this.reversed&&(i=i.split("").map((function(t){return Ga[t]})).join(""));const n=t.features.bpStart,r=1+t.bpStart+t.pixelWidth*t.bpPerPixel;for(let s=Math.floor(t.bpStart);s<=r;s++){const r=Math.floor(s-n);if(r>=0&&r.1)na.fillRect(e,n,5,o,10,{fillStyle:l});else{const i=n+.5*(o-e.measureText(a).width);"y"===t.axis?(e.save(),na.labelTransformWithContext(e,i),na.strokeText(e,a,i,15,{strokeStyle:l}),e.restore()):na.strokeText(e,a,i,15,{strokeStyle:l})}}}if(this.frameTranslate){let r=25;const s=this.translateSequence(i);for(let i=0;it.pixelWidth)break;let f=l.aminoA;l.aminoA.indexOf("STOP")>-1?(a="rgb(255, 0, 0)",f="STOP"):"M"===l.aminoA&&(a="rgb(0, 153, 0)",f="START"),na.fillRect(e,c,r,u-c,25,{fillStyle:a}),t.bpPerPixel<=.1&&na.strokeText(e,f,d-e.measureText(f).width/2,r+15)}r+=30}}}}get supportsWholeGenome(){return!1}computePixelHeight(t){return this.height=this.frameTranslate?Qa:25,this.height}fillColor(t){return this.color?this.color:"dna"===this.sequenceType?$a[t]||"gray":"rgb(0, 0, 150)"}getState(){const t={type:"sequence"};return this.order!==qa&&(t.order=this.order),this.reversed&&(t.revealed=!0),t}}class Ka{constructor(t,e){this.config=t,this.genome=e}async init(){this.fasta=await ja(this.config),this.chrNameMap=new Map;for(let t of this.fasta.chromosomeNames)this.chrNameMap.set(this.genome.getChromosomeName(t),t)}async getSequence(t,e,i){const n=this.chrNameMap.has(t)?this.chrNameMap.get(t):t;return this.fasta.getSequence(n,e,i)}}class Ja{constructor(t,e,i,n){this.guid=_e.guid(),this.trackView=t,this.referenceFrame=i,this.browser=t.browser,this.$viewport=fe('
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n.setAttribute("id",r),n.setAttribute("width",t.width),n.setAttribute("height",t.height),"CANVAS"===t.nodeName||"IMG"===t.nodeName?(i=this.__createElement("image"),i.setAttribute("width",t.width),i.setAttribute("height",t.height),i.setAttributeNS("http://www.w3.org/1999/xlink","xlink:href","CANVAS"===t.nodeName?t.toDataURL():t.getAttribute("src")),n.appendChild(i),this.__defs.appendChild(n)):t instanceof ll&&(n.appendChild(t.__root.childNodes[1]),this.__defs.appendChild(n)),new al(n,this)}setLineDash(t){t&&t.length>0?this.lineDash=t.join(","):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}const hl=function(t,e,i,n){this.start=t,this.end=e,this.name=i,this.stain=0,"acen"===n?this.type="c":(this.type=n.charAt(1),"p"===this.type&&(this.stain=parseInt(n.substring(4))))};const cl=qi,ul={loadGenome:async function(t){const e=t.cytobandURL,i=t.aliasURL,n=await ja(t);let r;i&&(r=await function(t,e){return zo.loadString(t,la(e)).then((function(t){var e=cl(t),i=[];return e.forEach((function(t){!t.startsWith("#")&&t.length>0&&i.push(t.split("\t"))})),i}))}(i,n.config));const s=new dl(t,n,r);return e&&(s.cytobands=await async function(t,e,i){let n;if(fa(t)){const e=bo(t);n="";const i=e.length;for(let t=0;t1?function(t,e){let i;if(e.chromosomeOrder)Array.isArray(e.chromosomeOrder)?t.wgChromosomeNames=e.chromosomeOrder:t.wgChromosomeNames=e.chromosomeOrder.split(",").map((t=>t.trim())),i=t.wgChromosomeNames.map((e=>t.chromosomes[e])).filter((t=>void 0!==t));else{const e=Object.keys(t.chromosomes).map((e=>t.chromosomes[e].bpLength)).reduce(((t,e)=>Math.max(t,e)))/50;i=Object.values(t.chromosomes).filter((t=>t.bpLength>e));const n=i.filter((t=>r(t.name.replace("chr","")))),s=i.filter((t=>!r(t.name.replace("chr",""))));n.sort(((t,e)=>Number.parseInt(t.name.replace("chr",""))-Number.parseInt(e.name.replace("chr",""))));const o=n.map((t=>t.name));for(let t of s)o.push(t.name);t.wgChromosomeNames=o}const n=i.reduce(((t,e)=>t+e.bpLength),0);function r(t){return/^\d+$/.test(t)}t.chromosomes.all={name:"all",bpLength:n}}(this,t):this.wgChromosomeNames=e.chromosomeNames;var n={},r=this;n.all="all",this.chromosomeNames.forEach((function(t){var e=t.startsWith("chr")?t.substring(3):"chr"+t;n[e.toLowerCase()]=t,"chrM"===t&&(n.mt="chrM"),"MT"===t&&(n.chrm="MT"),n[t.toLowerCase()]=t})),i&&i.forEach((function(t){var e,i;for(i=0;it.bpLength)&&(t=i)}return t}}getChromosomes(){return this.chromosomes}getGenomeCoordinate(t,e){var i=this.getCumulativeOffset(t);if(void 0!==i)return i+e}getChromosomeCoordinate(t){let e;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let i=0;for(let n of this.wgChromosomeNames){const r=this.cumulativeOffsets[n];if(r>t)return{chr:e,position:t-i};e=n,i=r}return{chr:this.wgChromosomeNames[this.wgChromosomeNames.length-1],position:0}}getCumulativeOffset(t){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let t=this,e={},i=0;for(let n of t.wgChromosomeNames)e[n]=Math.floor(i),i+=t.getChromosome(n).bpLength;return e}.call(this));const e=this.getChromosomeName(t);return this.cumulativeOffsets[e]}getGenomeLength(){let t=this;if(!this.bpLength){let e=0;t.wgChromosomeNames.forEach((function(i){let n=t.chromosomes[i];e+=n.bpLength})),this.bpLength=e}return this.bpLength}async getSequence(t,e,i){return t=this.getChromosomeName(t),this.sequence.getSequence(t,e,i)}addFeaturesToDB(t,e){const i=(t,e)=>{const i=this.featureDB.get(t);i&&(e=e.end-e.start>i.end-i.start?e:i),this.featureDB.set(t,e)};for(let n of t)if(n.name&&i(n.name.toUpperCase(),n),n.gene&&n.gene.name&&i(n.gene.name.toUpperCase(),n),e.searchableFields)for(let t of e.searchableFields){const e=n.getAttributeValue(t);e&&(e.indexOf(" ")>0?i(e.replaceAll(" ","+").toUpperCase(),n):i(e.toUpperCase(),n))}}}let fl,pl=0,gl=0;class ml extends Ja{constructor(t,e,i,n){super(t,e,i,n)}initializationHelper(){this.$spinner=fe("
",{class:"igv-loading-spinner-container"}),this.$viewport.append(this.$spinner),this.$spinner.append(fe("
"));const t=this.trackView.track;"sequence"!==t.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$viewport)),t.name&&"sequence"!==t.id&&(this.$trackLabel=fe('
'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(t.name),!1===this.browser.trackLabelsVisible&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(t){super.setContentHeight(t),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(t){this.$trackLabel.empty(),this.$trackLabel.html(t);const e=this.$trackLabel.text();this.$trackLabel.attr("title",e)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&"sequence"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>10)return fe(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if("all"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const t=this.trackView.track.visibilityWindow;return void 0!==t&&t>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>t}return!0})()){if(this.canvas&&(fe(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const t=this.trackView.minHeight||0;this.setContentHeight(t)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const t=this.referenceFrame;if(this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===t.bpPerPixel){const e=Math.round((this.canvas._data.bpStart-t.start)/t.bpPerPixel);this.canvas.style.left=e+"px"}}setTop(t){if(super.setTop(t),this.canvas){const e=this.$viewport.height(),i=t+this.canvas._data.pixelTop,n=i+this.canvas._data.pixelHeight;(i>0||n0)for(let n of i.roiSets){const i=await n.getFeatures(e,r,s,t.bpPerPixel);o.push({track:n,features:i})}const a=i&&("wig"===i.type||"merged"===i.type);return this.featureCache=new bl(e,r,s,t.bpPerPixel,n,o,a),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}}catch(t){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage("Error loading track data"),this.browser.alert.present(t),console.error(t))}finally{this.loading=!1,this.stopSpinner()}}}repaintDimensions(){const t=ul.isWholeGenomeView(this.referenceFrame.chr),e=t?this.$viewport.width():3*this.$viewport.width(),i=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(t?0:e/3*i),bpEnd:this.referenceFrame.end+(t?0:e/3*i),pixelWidth:e}}repaint(){if(void 0===this.featureCache)return;const{features:t,roiFeatures:e}=this.featureCache,{bpStart:i,bpEnd:n,pixelWidth:r}=this.repaintDimensions(),s=this.$viewport.height(),o=this.getContentHeight(),a=e?Math.max(o,s):o,l=Math.min(a,3*s);if(0===r||0===l)return void(this.canvas&&fe(this.canvas).remove());const h=Math.max(0,-this.contentTop-Math.floor(l/3)),c=this.referenceFrame.bpPerPixel,u=Math.round((i-this.referenceFrame.start)/c),d=(this.contentTop||0)+h,f=document.createElement("canvas");f.style.position="relative",f.style.display="block",f.style.width=r+"px",f.style.height=l+"px",f.style.left=u+"px",f.style.top=d+"px";const p="FILL"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=p*r,f.height=p*l;const g=f.getContext("2d");g.scale(p,p),g.translate(0,-h);const m={context:g,pixelXOffset:u,pixelWidth:r,pixelHeight:l,pixelTop:h,bpStart:i,bpEnd:n,bpPerPixel:c,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(m,t,e),this.canvas&&fe(this.canvas).remove(),f._data=m,this.canvas=f,this.$viewport.append(fe(f))}refresh(){if(!this.canvas||!this.featureCache)return;const t=this.canvas._data;t.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:e,roiFeatures:i}=this.featureCache;this.draw(t,e,i)}draw(t,e,i){if(e&&(t.features=e,this.trackView.track.draw(t)),i&&i.length>0)for(let e of i)t.features=e.features,e.track.draw(t)}containsPosition(t,e){return this.referenceFrame.chr===t&&e>=this.referenceFrame.start&&e<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const t=this.canvas._data,e=t?t.pixelTop:0,i=window.devicePixelRatio,n=this.$viewport.width()*i,r=this.$viewport.height()*i,s=-fe(this.canvas).position().left*i,o=(-this.contentTop-e)*i,a=this.canvas.getContext("2d").getImageData(s,o,n,r),l=document.createElement("canvas"),h=l.getContext("2d");l.width=a.width,l.height=a.height,h.putImageData(a,0,0),Qi((this.$trackLabel.text()?this.$trackLabel.text():"image")+".png",l.toDataURL("image/png"))}saveSVG(){let{width:t,height:e}=this.browser.columnContainer.getBoundingClientRect();const i=new ll({width:t,height:8e3,backdropColor:"white",multiLocusGap:0,viewbox:{x:0,y:0,width:t,height:8e3}});this.renderViewportToSVG(i,{deltaX:32,deltaY:32}),i.setHeight(e);const n=(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,""),r=this.browser.referenceFrameList.indexOf(this.referenceFrame),s=i.getSerializedSvg(!0),o=URL.createObjectURL(new Blob([s],{type:"application/octet-stream"}));Qi(`${n}_referenceFrame_${r}_guid_${_e.guid()}.svg`,o)}renderViewportToSVG(t,{deltaX:e,deltaY:i}){if(this.$zoomInNotice&&this.$zoomInNotice.is(":visible"))return;const{width:n,height:r}=this.$viewport.get(0).getBoundingClientRect(),s=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${_e.guid()}`;this.drawSVGWithContext(t,n,r,s,e,i+this.contentTop,-this.contentTop)}renderSVGContext(t,{deltaX:e,deltaY:i}){if(this.renderViewportToSVG(t,{deltaX:e,deltaY:i}),(!this.$zoomInNotice||!this.$zoomInNotice.is(":visible"))&&this.$trackLabel&&!0===this.browser.trackLabelsVisible){const{x:n,y:r,width:s,height:o}=_e.relativeDOMBBox(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(t,e+n,i+r,s,o)}}renderTrackLabelSVG(t,e,i,n,r){const s=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_track_label_guid_${_e.guid()}`;t.saveWithTranslationAndClipRect(s,e,i,n,r,0),t.fillStyle="white",t.fillRect(0,0,n,r),t.font="12px Arial",t.fillStyle="rgb(68, 68, 68)";const{width:o}=t.measureText(this.$trackLabel.text()),a=.25*(n-o),l=.7*(r-12);t.fillText(this.$trackLabel.text(),a,r-l),t.strokeStyle="rgb(68, 68, 68)",t.strokeRect(0,0,n,r),t.restore()}drawSVGWithContext(t,e,i,n,r,s,o){t.saveWithTranslationAndClipRect(n,r,s,e,i,o);let{start:a,bpPerPixel:l}=this.referenceFrame;const h={context:t,viewport:this,referenceFrame:this.referenceFrame,top:o,pixelTop:o,pixelWidth:e,pixelHeight:i,bpStart:a,bpEnd:a+e*l,bpPerPixel:l,viewportWidth:e,selection:this.selection},c=this.featureCache?this.featureCache.features:void 0,u=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(h,c,u),t.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(t,e,i,n,r){if(this.featureCache&&this.featureCache.containsRange(e,i,n,r))return this.featureCache.features;if("function"==typeof t.getFeatures){const s=await t.getFeatures(e,i,n,r,this);return this.checkContentHeight(s),s}}needsRepaint(){if(!this.canvas)return!0;const t=this.canvas._data;return!t||this.referenceFrame.startt.bpEnd||this.referenceFrame.chr!==t.referenceFrame.chr||this.referenceFrame.bpPerPixel!=t.bpPerPixel}needsReload(){if(!this.featureCache)return!0;const{chr:t,bpPerPixel:e}=this.referenceFrame,{bpStart:i,bpEnd:n}=this.repaintDimensions();return!this.featureCache.containsRange(t,i,n,e)}createZoomInNotice(t){const e=fe("
",{class:"igv-zoom-in-notice-container"});t.append(e);const i=fe("
");return e.append(i),i.text("Zoom in to see features"),e.hide(),e}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const t=this.$viewport.get(0);this.addViewportContextMenuHandler(t);const e=t=>{this.enableClick=!0,this.browser.mouseDownOnViewport(t,this),_e.pageCoordinates(t)};t.addEventListener("mousedown",e),t.addEventListener("touchstart",e);const i=t=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};t.addEventListener("mouseup",i),t.addEventListener("touchend",i),"function"==typeof this.trackView.track.hoverText&&t.addEventListener("mousemove",(t=>{if(0===t.buttons&&Date.now()-gl>100){gl=Date.now();const e=this.createClickState(t);if(e){const t=this.trackView.track.hoverText(e);t?this.$viewport[0].setAttribute("title",t):this.$viewport[0].removeAttribute("title")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&"sequence"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(t){t.addEventListener("contextmenu",(t=>{if(this.browser.dragObject)return!1;const e=this.createClickState(t);if(void 0===e)return!1;t.preventDefault();let i=[];if("function"==typeof this.trackView.track.contextMenuItemList){const t=this.trackView.track.contextMenuItemList(e);t&&(i=t)}i.length>0&&i.push({label:fe("
")}),i.push({label:"Save Image (PNG)",click:()=>this.savePNG()}),i.push({label:"Save Image (SVG)",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(t,i)}))}addViewportClickHandler(t){t.addEventListener("click",(t=>{if(this.enableClick&&this.canvas){if(3===t.which||t.ctrlKey)return;if(fe(".igv-popover").hide(),this.browser.dragObject||this.browser.isScrolling)return;t.preventDefault();const e=_e.translateMouseCoordinates(t,this.$viewport.get(0)).x,i=_e.translateMouseCoordinates(t,this.canvas).x,n=this.referenceFrame,r=Math.floor(n.start+n.toBP(i)),s=Date.now();if(s-plt));t[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=e,i=t.join(" ")}this.browser.search(i)}else this.browser.zoomWithScaleFactor(.5,t,this.referenceFrame)}else t.shiftKey&&"function"==typeof this.trackView.track.shiftClick?this.trackView.track.shiftClick(r,t):"function"==typeof this.trackView.track.popupData&&(fl=setTimeout((()=>{const e=this.getPopupContent(t);e&&(this.popover&&this.popover.dispose(),this.popover=new Oi(this.browser.columnContainer),this.popover.presentContentWithEvent(t,e)),window.clearTimeout(fl),fl=void 0}),this.browser.constants.doubleClickDelay));pl=s}}))}addTrackLabelClickHandler(t){t.addEventListener("click",(t=>{t.stopPropagation();const{track:e}=this.trackView;let i;"function"==typeof e.description?i=e.description():e.description&&(i=`
${e.description}
`),i&&(this.popover&&this.popover.dispose(),this.popover=new Oi(this.browser.columnContainer,e.name||""),this.popover.presentContentWithEvent(t,i))}))}createClickState(t){if(!this.canvas)return;const e=this.referenceFrame,i=_e.translateMouseCoordinates(t,this.$viewport.get(0)),n=_e.translateMouseCoordinates(t,this.canvas),r=e.start+e.toBP(i.x);return{event:t,viewport:this,referenceFrame:e,genomicLocation:r,y:i.y-this.contentTop,canvasX:n.x,canvasY:n.y}}getPopupContent(t){const e=this.createClickState(t);if(void 0===e)return;let i=this.trackView.track;const n=i.popupData(e),r=this.browser.fireEvent("trackclick",[i,n]);let s;return void 0===r||!0===r?n&&n.length>0&&(s=n.map((t=>{if(t.name){const e=`${t.name}   ${t.value}`;return`
${e}
`}return"
"===t?t:t.html?t.html:`
${t}
`})).join("")):"string"==typeof r&&(s=r),s}}class bl{constructor(t,e,i,n,r,s,o){this.chr=t,this.bpStart=e,this.bpEnd=i,this.bpPerPixel=n,this.features=r,this.roiFeatures=s,this.multiresolution=o}containsRange(t,e,i,n){const r=this.multiresolution?this.bpPerPixel/n:1;return e>=this.bpStart&&i<=this.bpEnd&&t===this.chr&&r>.5&&r<2}overlapsRange(t,e,i){return this.chr===t&&i>=this.bpStart&&e<=this.bpEnd}}function yl(t,e){if(!(t.length<6))return{chr:t[0],start:t[1],end:t[2],chr1:t[8],start1:Number.parseInt(t[9]),end1:Number.parseInt(t[10]),chr2:t[13],start2:Number.parseInt(t[14]),end2:Number.parseInt(t[15]),name:t[3],score:Number(t[4]),value:Number(t[5]),color:"."===t[7]?void 0:"0"===t[7]?"rgb(0,0,0)":t[7]};console.log("Skipping line: "+t.join(" "))}const vl=new Set(["transcript","primary_transcript","processed_transcript","mRNA","mrna","lnc_RNA","miRNA","ncRNA","rRNA","scRNA","snRNA","snoRNA","tRNA"]),wl=new Set(["CDS","cds"]),_l=new Set(["start_codon","stop_codon"]),xl=new Set(["5UTR","3UTR","UTR","five_prime_UTR","three_prime_UTR","3'-UTR","5'-UTR"]),kl=new Set(["exon","coding-exon"]),Sl=new Set;for(let _y of[wl,_l,xl,kl])for(let xy of _y)Sl.add(xy);function Cl(t){return t.includes("intron")}function Al(t){return wl.has(t)||_l.has(t)}function Tl(t){return xl.has(t)}function Il(t){return vl.has(t)||t.endsWith("RNA")||t.endsWith("transcript")}function El(t){return Sl.has(t)||t.endsWith("RNA")||Cl(t)}const Ml=new Set(["id","parent","name"]);class Rl{constructor(t){Object.assign(this,t)}popupData(t){const e=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&e.push("
"),this.name&&e.push({name:"Name",value:this.name}),e.push({name:"Type",value:this.type}),e.push({name:"Source",value:this.source}),void 0!==this.score&&e.push({name:"Score",value:this.score}),this.attributeString){const t=Ol(this.attributeString,this.delim);for(let[i,n]of t)void 0!==n&&n.length>0&&!Ml.has(i.toLowerCase())&&e.push({name:i+":",value:n})}return e.push({name:"Location",value:`${this.chr}:${$i(this.start+1)}-${$i(this.end)}`}),e}getAttributeValue(t){if(this.hasOwnProperty(t))return this[t];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(t))return this._attributeCache.get(t);{const e=Ol(this.attributeString,this.delim);let i;for(let[n,r]of e)if(n===t){i=r;break}return this._attributeCache.set(t,i),i}}}class Ll extends Rl{constructor(t){super(t),this.exons=[],this.parts=[]}addExon(t){this.exons.push(t),this.start=Math.min(this.start,t.start),this.end=Math.max(this.end,t.end)}addPart(t){this.parts.push(t)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(t,e){return t.start-e.start}));let t=this.parts[0].start,e=this.parts[0].end;for(let i=1;i=e&&i.start<=t)return i}addCDS(t){let e;const i=this.exons;for(let n of i)if(n.start<=t.start&&n.end>=t.end){e=n;break}e?(e.cdStart=e.cdStart?Math.min(t.start,e.cdStart):t.start,e.cdEnd=e.cdEnd?Math.max(t.end,e.cdEnd):t.end):console.error("No exon found spanning "+t.start+"-"+t.end),this.cdStart=this.cdStart?Math.min(t.start,this.cdStart):t.start,this.cdEnd=this.cdEnd?Math.max(t.end,this.cdEnd):t.end}addUTR(t){let e;const i=this.exons;for(let n=0;n=t.end){e=i[n];break}e?t.start===e.start&&t.end===e.end?e.utr=!0:(t.ende.start&&(e.cdEnd=t.start)):console.error("No exon found spanning "+cds.start+"-"+cds.end)}finish(){this.assembleParts();var t=this.cdStart,e=this.cdEnd;this.exons.sort((function(t,e){return t.start-e.start})),t&&this.exons.forEach((function(i){(i.ende)&&(i.utr=!0)}))}popupData(t){const e=super.popupData(t);for(let i of this.exons)if(!i.pseudo&&t>=i.start&&t");const n=i.popupData(t);for(let t of n)e.push(t)}for(let i of this.parts)if(t>=i.start&&t");const n=i.popupData(t);for(let t of n)e.push(t)}return e}}function Bl(t,e){const i=e.format;if(t.length<9)return;const n="gff3"===i?"=":" ";return new Rl({source:zl(t[1]),type:t[2],chr:t[0],start:parseInt(t[3])-1,end:parseInt(t[4]),score:"."===t[5]?void 0:Number(t[5]),strand:t[6],phase:"."===t[7]?0:parseInt(t[7]),attributeString:t[8],delim:n})}function Nl(t,e){const i=Bl(t,e);if(!i)return;const n=Ol(i.attributeString,i.delim);for(let[t,e]of n){const n=t.toLowerCase();"color"===n||"colour"===n?i.color=xo.createColorString(e):"ID"===t?i.id=e:"Parent"===t&&(i.parent=e)}return i}function Fl(t,e){const i=Bl(t,e);if(!i)return;const n=Ol(i.attributeString,i.delim);let r,s;switch(i.type){case"gene":r="gene_id";break;case"transcript":r="transcript_id",s="gene_id";break;default:s="transcript_id"}for(let[t,e]of n){const n=t.toLowerCase();"color"===n||"colour"===n?i.color=xo.createColorString(e):t===r?i.id=e:t===s&&(i.parent=e)}return i}function Ol(t,e,i=!1){var n=[];for(let r of t.split(";")){r=r.trim();const t=r.indexOf(e);if(t>0&&t2?parseInt(t[2]):n+1;if(isNaN(n)||isNaN(r))return new Ul("Unparsable bed record.");const s=new Jl({chr:i,start:n,end:r,score:1e3});try{if(t.length>3){if(t[3].indexOf(";")>0&&t[3].indexOf("=")>0){const i=Ol(t[3],"=",!0);s.attributes={};for(let t of i)s.attributes[t[0]]=t[1],null!=e.nameField&&t[0]===e.nameField&&(s.name=t[1])}s.name||(s.name="."===t[3]?"":t[3])}if(t.length>4&&(s.score="."===t[4]?0:Number(t[4]),isNaN(s.score)))return s;if(t.length>5&&(s.strand=t[5],"."!==s.strand&&"+"!==s.strand&&"-"!==s.strand))return s;if(t.length>6&&(s.cdStart=parseInt(t[6]),isNaN(s.cdStart)))return s;if(t.length>7&&(s.cdEnd=parseInt(t[7]),isNaN(s.cdEnd)))return s;if(t.length>8&&"."!==t[8]&&"0"!==t[8]&&(s.color=xo.createColorString(t[8])),t.length>11){const e=parseInt(t[9]);if(e>1e3)return s;const i=t[10].replace(/,$/,"").split(","),r=t[11].replace(/,$/,"").split(",");if(i.length!==r.length||e!==i.length)return s;const o=[];for(let t=0;t0&&(Zl(o,s.cdStart,s.cdEnd),s.exons=o)}if(e){let i=e.thicknessColumn,n=e.colorColumn;n&&ni?n.utr=!0:(e>=r&&e<=t&&(n.cdStart=e),i>=r&&i<=t&&(n.cdEnd=i))}}function Yl(t,e){var i,n,r,s,o,a,l;if(!(t.length<9))return i=t[0],n=parseInt(t[1]),r=parseInt(t[2]),o=t[3],a=Number(t[4]),s=t[5].trim(),l=Number(t[6]),0===a&&(a=l),{chr:i,start:n,end:r,name:o,score:a,strand:s,signal:l,pValue:Number(t[7]),qValue:Number(t[8])}}function Ql(t,e){if(t.length<=3)return;const i={chr:t[0],start:parseInt(t[1]),end:parseInt(t[2]),value:Number(t[3])};if(e){let n=e.colorColumn;n&&n0)for(var d=l.split(","),f=0;fu&&(u=m),h.spanning_frag_coords.push({left:g,right:m})}return h.start=c,h.end=u,h}}function ih(t,e){if(t.length<7)return null;const i={chr:t[0],start:parseInt(t[1])-1,end:parseInt(t[2]),"Strongest SNP-risk allele":t[3],"Disease/Phenotype":t[4],"P-value":t[5],"Odds ratio or beta":t[6]};return t.length>6&&(i.PUBMEDID=`${t[7]}`),i}function nh(t,e){const i=e.customFormat;if(t.length1&&(e=t)}else{this.setDecoder(n.format);const t=i.split(this.delimiter||"\t");try{const i=Object.assign({columnNames:e},n);if(this.decode(t,i))break;t.length>1&&(e=t)}catch(i){t.length>1&&(e=t)}}}if(e){n.columnNames=e;for(let t=0;t0&&console.error(`Error parsing line '${s}': ${l.message}`)):l&&e.push(l)}return i===ya&&function(t){if(0==t.length)return;const e=t[0];if(void 0===e.score&&void 0!==e.name){for(let e of t)if(!("number"==typeof(i=e.name)?i-i==0:"string"==typeof i&&""!==i.trim()&&(Number.isFinite?Number.isFinite(+i):isFinite(+i)))&&"."!==e.name)return;for(let e of t)e.score=Number(e.name),delete e.name}var i;const n=t.filter((t=>t.chr1!==t.chr2));for(let e of n){const i=Object.assign({},e);i.dup=!0,t.push(i),e.chr=e.chr1,e.start=e.start1,e.end=e.end1,i.chr=i.chr2,i.start=i.start2,i.end=i.end2}}(e),e}setDecoder(t){switch(t){case"narrowpeak":case"broadpeak":case"regionpeak":case"peaks":this.decode=Yl,this.delimiter=this.config.delimiter||/\s+/;break;case"bedgraph":this.decode=Ql,this.delimiter=/\s+/;break;case"wig":this.decode=Xl,this.delimiter=this.config.delimiter||/\s+/;break;case"gff3":case"gff":this.decode=Nl,this.delimiter="\t";break;case"gtf":this.decode=Fl,this.delimiter="\t";break;case"fusionjuncspan":this.decode=eh,this.delimiter=this.config.delimiter||/\s+/;break;case"gtexgwas":this.skipRows=1,this.decode=ih,this.delimiter="\t";break;case"refflat":this.decode=ql,this.delimiter=this.config.delimiter||/\s+/;break;case"genepred":this.decode=jl,this.delimiter=this.config.delimiter||/\s+/;break;case"genepredext":this.decode=$l,this.delimiter=this.config.delimiter||/\s+/;break;case"ensgene":this.decode=jl,this.header.shift=1,this.delimiter=this.config.delimiter||/\s+/;break;case"refgene":this.decode=$l,this.delimiter=this.config.delimiter||/\s+/,this.header.shift=1;break;case"bed":this.decode=Vl,this.delimiter=this.config.delimiter||/\s+/;break;case"bedpe":case"hiccups":this.decode=ya,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-domain":this.decode=va,this.headerLine=!0,this.delimiter=this.config.delimiter||"\t";break;case"bedpe-loop":this.decode=ya,this.delimiter=this.config.delimiter||"\t",this.header={colorColumn:7};break;case"interact":this.decode=yl,this.delimiter=this.config.delimiter||/\s+/;break;case"snp":this.decode=Kl,this.delimiter="\t";break;case"rmsk":this.decode=Hl,this.delimiter="\t";break;case"gcnv":this.decode=rh,this.delimiter="\t";break;default:const e=xa(t);void 0!==e?(this.decode=nh,this.header.customFormat=e,this.delimiter=e.delimiter||"\t"):(this.decode=Vl,this.delimiter=this.config.delimiter||/\s+/)}}}function oh(t){const e={},i=t.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g);let n;const r=[];for(let t of i)t&&0!==t.trim().length&&(t.endsWith("=")?n=t:n?(r.push(n+t),n=void 0):r.push(t));for(let t of r){if(!t)return;var s=t.split("=",2);if(2===s.length){const t=s[0].trim(),i=s[1].trim();if(e.hasOwnProperty(t)){let n=e[t];Array.isArray(n)?n.push(i):e[t]=[n,i]}else e[t]=i}}return"interact"==e.type?e.format="interact":"gcnv"===e.type&&(e.format="gcnv"),e}function ah(t){let e={},i=t.split(/\s+/);return 2===i.length&&i[1].split(";").forEach((function(t){let i=t.split("=");"color"===i[0]?e.colorColumn=Number.parseInt(i[1])-1:"thickness"===i[0]&&(e.thicknessColumn=Number.parseInt(i[1])-1)})),e}function lh(t){const e=t.split(/\s+/);return{format:"fixedStep",chrom:e[1].split("=")[1],start:parseInt(e[2].split("=")[1],10)-1,step:parseInt(e[3].split("=")[1],10),span:e.length>4?parseInt(e[4].split("=")[1],10):1,index:0}}function hh(t){const e=t.split(/\s+/);return{format:"variableStep",chrom:e[1].split("=")[1],span:e.length>2?parseInt(e[2].split("=")[1],10):1}}class ch{static defaults={height:50,autoHeight:!1,visibilityWindow:void 0,color:void 0,altColor:void 0,supportHiDPI:!0};constructor(t,e){this.browser=e,this.init(t)}init(t){this.config=t,t.displayMode&&(t.displayMode=t.displayMode.toUpperCase());const e=Object.assign({},ch.defaults);if(this.constructor.defaults)for(let t of Object.keys(this.constructor.defaults))e[t]=this.constructor.defaults[t];for(let n of Object.keys(e))this[n]=t.hasOwnProperty(n)?t[n]:e[n],"color"!==n&&"altColor"!==n||(this[n]=ji(i=this[n])&&i.indexOf(",")>0&&!i.startsWith("rgb(")&&!i.startsWith("rgba(")?`rgb(${i})`:i);var i;t.name||t.label?this.name=t.name||t.label:Yi(t.url)?this.name=t.url.name:ji(t.url)&&!t.url.startsWith("data:")&&(this.name=Zi(t.url)),this.url=t.url,this.config.type&&(this.type=this.config.type),this.id=void 0===this.config.id?this.name:this.config.id,this.order=t.order,this.autoscaleGroup=t.autoscaleGroup,this.removable=void 0===t.removable||t.removable,this.minHeight=t.minHeight||Math.min(25,this.height),this.maxHeight=t.maxHeight||Math.max(1e3,this.height),t.onclick&&(this.onclick=t.onclick,t.onclick=void 0),t.description&&("function"==typeof t.description?this.description=t.description:this.description=()=>t.description),t.hoverTextFields?this.hoverText=uh.bind(this):"function"==typeof this.config.hoverText&&(this.hoverText=this.config.hoverText)}get name(){return this._name}set name(t){this._name=t,this.trackView&&this.trackView.setTrackLabelName(t)}updateConfig(t){this.init(t)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}getState(){const t={};for(let i of Object.keys(this.config))i.startsWith("_")||void 0===(e=this.config[i])||"function"==typeof e||e instanceof File||e instanceof Promise||(t[i]=this.config[i]);var e;for(let e of Object.keys(t)){if(e.startsWith("_"))continue;const i=this[e];i&&(aa(i)||"boolean"==typeof i||"metadata"===e)&&(t[e]=i)}const i=ch.defaults;if(this.constructor.defaults)for(let t of Object.keys(this.constructor.defaults))i[t]=this.constructor.defaults[t];for(let e of Object.keys(i))void 0!==this[e]&&i[e]!==this[e]&&(t[e]=this[e]);return!this.autoscale&&this.dataRange&&(t.min=this.dataRange.min,t.max=this.dataRange.max),t}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(t){if(this.disposed)return;const e={};let i;for(let n of Object.keys(t))switch(n.toLowerCase()){case"usescore":e.useScore=1===t[n]||"1"===t[n]||"on"===t[n]||!0===t[n];break;case"visibility":switch(t[n]){case"2":case"3":case"pack":case"full":e.displayMode="EXPANDED";break;case"4":case"squish":e.displayMode="SQUISHED";break;case"1":case"dense":e.displayMode="COLLAPSED"}break;case"color":case"altcolor":e[n]=t[n].startsWith("rgb(")?t[n]:"rgb("+t[n]+")";break;case"featurevisiblitywindow":case"visibilitywindow":e.visibilityWindow=Number.parseInt(t[n]);break;case"maxheightpixels":i=t[n].split(":"),3===i.length&&(e.minHeight=Number.parseInt(i[2]),e.height=Number.parseInt(i[1]),e.maxHeight=Number.parseInt(i[0]));break;case"viewlimits":if(!this.config.autoscale){i=t[n].split(":");let r,s=0;1==i.length?r=Number(i[0]):2==i.length&&(s=Number(i[0]),r=Number(i[1])),e.autoscale=!1,e.dataRange={min:s,max:r},this.viewLimitMin=s,this.viewLimitMax=r}case"name":e[n]=t[n];break;case"url":e.infoURL=t[n];break;case"type":const r=t[n];dh.has(r)?e[n]=dh.get(r):e[n]=r;break;case"graphtype":e.graphType=t[n];break;default:e[n]=t[n]}for(let t of Object.keys(e))if(!this.config.hasOwnProperty(t)||"name"===t&&this.config._derivedName){let i=e[t];if("true"===i&&(i=!0),"false"===i&&(i=!1),this[t]=i,"height"===t&&this.trackView)try{const t=Number.parseInt(i);this.trackView.setTrackHeight(t)}catch(t){console.error(t)}}}clickedFeatures(t){const e=t.viewport.cachedFeatures;if(!e||!Array.isArray(e)||0===e.length)return[];const i=t.genomicLocation,n=t.referenceFrame.bpPerPixel>.2?3*t.referenceFrame.bpPerPixel:.2;return Xo(e,i-n,i+n)}extractPopupData(t,e){const i=new Set(["row","color","chr","start","end","cdStart","cdEnd","strand","alpha"]),n=[];let r,s;for(let e in t)if(t.hasOwnProperty(e)&&!i.has(e)&&aa(t[e])){let i=t[e];n.push({name:Gi(e),value:i}),"alleles"===e?r=t[e]:"alleleFreqs"===e&&(s=t[e])}if(r&&s){r.endsWith(",")&&(r=r.substr(0,r.length-1)),s.endsWith(",")&&(s=s.substr(0,s.length-1));let i=r.split(","),o=s.split(",");if(o.length>1){let r=[];for(let t=0;t=0;i--){let o=r[i].a;if(1===o.length){e||(e=this.getGenomeId());const i=ch.getCravatLink(t.chr,t.start+1,s,o,e);console.log(i),i&&(n.push("
"),n.push({html:i}),n.push("
"))}}}}if(t.attributes)for(let e of Object.keys(t.attributes))n.push({name:e,value:t.attributes[e]});let o=`${t.chr}:${$i(t.start+1)}-${$i(t.end)}`;return t.strand&&(o+=` (${t.strand})`),n.push({name:"Location",value:o}),n}description(){const t=(t,e)=>`
${t}: ${e}
`;let e='
';if(this.url?Yi(this.url)?e+=t("Filename",this.url.name):e+=t("URL",this.url):e=this.name,this.config){if(this.config.metadata)for(let i of Object.keys(this.config.metadata))e+=t(i,this.config.metadata[i]);for(let i of Object.keys(this.config)){if(i.startsWith("_"))continue;let n=i.substr(0,1);if(n!==n.toLowerCase()){const n=this.config[i];n&&aa(n)&&(e+=t(i,n))}}}return e+="
",e}getColorForFeature(t){return"function"==typeof this.color?this.color(feature):this.color}dispose(){this.disposed=!0;for(let t of Object.keys(this))this[t]=void 0}static getCravatLink(t,e,i,n,r){if("hg38"===r||"GRCh38"===r)return`Cravat ${i}->${n}`}}function uh(t){if(!this.hoverTextFields)return;const e=this.clickedFeatures(t);if(e&&e.length>0){let t="";for(let i=0;i0&&(t+="\n"),t="";for(let e of this.hoverTextFields)t.length>0&&(t+="\n"),n.hasOwnProperty(e)?t+=n[e]:"function"==typeof n.getAttribute&&(t+=n.getAttribute(e))}return t}}const dh=new Map([["wiggle_0","wig"],["bed","bed"],["bigBed","bigBed"],["bigWig","bigWig"]]);class fh{constructor(t){switch(this.type=t||"seg",this.type){case"mut":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case"maf":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(t){let e;for(;void 0!==(e=await t.nextLine());)if(!e.startsWith("#")){const t=e.split("\t");this.header={headings:t};break}return this.header}async parseFeatures(t){const e=[];let i;this.header||(this.header=await this.parseHeader(t)),"seg"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(i=this.extractExtraColumns(this.header.headings));const n=this.header.headings[this.dataColumn];let r;for(;void 0!==(r=await t.nextLine());){const t=r.split("\t"),s="seg"===this.type?Number(t[this.dataColumn]):t[this.dataColumn];if(t.length>this.dataColumn){const r=new ph({sample:t[this.sampleColumn],chr:t[this.chrColumn],start:parseInt(t[this.startColumn])-1,end:parseInt(t[this.endColumn]),value:s,valueColumnName:n});if(i){const e=this.extractExtraColumns(t);r.setAttributes({names:i,values:e})}e.push(r)}}return e}extractExtraColumns(t){const e=[];for(let i=0;i=0)return this.attributeValues[e]}}popupData(t,e){const i=new Set(["chr","start","end","sample","value","row","color","sampleKey","uniqueSampleKey","sampleId","chromosome","uniquePatientKey"]),n=this.chr+":"+$i(this.start+1)+"-"+$i(this.end),r=[{name:"Sample",value:this.sample},{name:"Location",value:n},{name:this.valueColumnName?Gi(this.valueColumnName):"Value",value:this.value}];if("mut"===t&&"hg38"===e){const t=this.extractCravatLink(e);t&&(r.push("
"),r.push({html:t}),r.push("
"))}if(this.attributeNames&&this.attributeNames.length>0)for(let t=0;t0)for(let n=0;n"===e||"<*>"===e||"."===e)return"NONVARIANT";{const t=e.split(",").map((function(t){return 1===i&&1===t.length?"SNP":""===t?"NONVARIANT":"OTHER"}));let n=t[0];for(let e of t)if(e!==n)return"MIXED";return n}}(t,e)),"NONVARIANT"===this.type&&(this.heterozygosity=0),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if("NONVARIANT"===this.type)this.start=this.pos-1,this.end=this.start+t.length;else{const i=e.split(",").filter((t=>t.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let e of i)if(this.alleles.push(e),"SV"!==this.type&&yh(e)){let i=e.length,n=t.length;const r=Math.min(i,n);let s=0;for(;s0&&n>0;){const r=s+i-1,o=s+n-1;if(e.charCodeAt(r)!==t.charCodeAt(o))break;i--,n--}for(;i>0&&n>0;){const r=s,o=s;if(e.charCodeAt(r)!==t.charCodeAt(o))break;s++,i--,n--}const o=this.pos+s-1,a=o+n;this.start=void 0===this.start?o:Math.min(this.start,o),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos)}}popupData(t,e){const i=`${$i(this.pos)}`,n=this.start===this.end?`${$i(this.start)} | ${$i(this.start+1)}`:`${$i(this.start+1)}-${$i(this.end)}`,r=[{name:"Chr",value:this.chr},{name:"Pos",value:i},{name:"Loc",value:n},{name:"ID",value:this.names?this.names:""},{name:"Ref",value:this.referenceBases},{name:"Alt",value:this.alternateBases.replace("<","<")},{name:"Qual",value:this.quality},{name:"Filter",value:this.filter}];if("SNP"===this.type){let t=this.referenceBases;if(1===t.length){let i=this.alternateBases.split(",");for(let n of i)if(1===n.length){let i=ch.getCravatLink(this.chr,this.pos,t,n,e);i&&(r.push("
"),r.push({html:i}))}}}if(this.hasOwnProperty("heterozygosity")&&r.push({name:"Heterozygosity",value:this.heterozygosity}),this.info){r.push({html:'
'});for(let t of Object.keys(this.info))r.push({name:t,value:vh(decodeURIComponent(this.info[t]))})}return r}getInfo(t){return this.info?this.info[t]:void 0}isRefBlock(){return"NONVARIANT"===this.type}}const bh=new Set(["A","C","T","G"].map((t=>t.charCodeAt(0))));function yh(t){for(let e=0;e");if(!(e>2&&o>0)){console.log("Malformed VCF header line: "+n);continue}const a=n.substring(2,e-1);i[a]||(i[a]={});const l=Wi(n.substring(e+1,o-1),",");for(let e of l){var r=e.split("=");r.length>1&&("ID"===r[0]?t=r[1]:s[r[0]]=r[1])}t&&(i[a][t]=s)}else if(n.startsWith("##contig")&&e){const t=n.indexOf("",t));const s=n.substring(t+4,r),o=e.getChromosomeName(s);i.chrAliasTable.set(o,s)}}else if(n.startsWith("#CHROM")){const t=n.split("\t");if(t.length>8){i.callSets=[];for(let e=9;e9){const e=_h(t[8].split(":"));n.calls={};for(let r=9;r0?n=t:n?(r.push(n+t),n=void 0):r.push(t));for(let t of r){if(!t)return;var s=t.split("=",2);if(2===s.length){const t=s[0].trim(),i=s[1].trim();e[t]=i}}return e}function Rh(t){let e={},i=t.split(/\s+/);return 2===i.length&&i[1].split(";").forEach((function(t){let i=t.split("=");"color"===i[0]?e.colorColumn=Number.parseInt(i[1])-1:"thickness"===i[0]&&(e.thicknessColumn=Number.parseInt(i[1])-1)})),e}function Lh(t,e){var i,n,r=t.columns;this.aed=t,this.allColumns=e,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=".",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let t=0;t0)for(let t=0;t=0;i--)e=256*e+t[i];else for(let i=0;i0&&(n+=String.fromCharCode(i));return n}getFixedLengthTrimmedString(t){var e,i,n="";for(e=0;e32&&(n+=String.fromCharCode(i));return n}getFloat(){var t=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,t}getDouble(){var t=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,t}skip(t){return this.position+=t,this.position}getVPointer(){var t=this.position,e=this.view.getUint8(t+1)<<8|this.view.getUint8(t),i=4294967296*(255&this.view.getUint8(t+6))+16777216*(255&this.view.getUint8(t+5))+65536*(255&this.view.getUint8(t+4))+256*(255&this.view.getUint8(t+3))+(255&this.view.getUint8(t+2));return this.position+=8,new Fh(i,e)}}class Fh{constructor(t,e){this.block=t,this.offset=e}isLessThan(t){return this.blockt.block||this.block===t.block&&this.offset>t.offset}isEqualTo(t){return this.block===t.block&&this.offset===t.offset}print(){return this.block+":"+this.offset}}function Oh(t,e){if(0===t.length)return t;if(t.sort((function(t,e){const i=t.minv.block-e.minv.block;return 0!==i?i:t.minv.offset-e.minv.offset})),t.length<=1)return t;e&&(t=t.filter((t=>t.maxv.isGreaterThan(e))));const i=[];let n;for(let e of t)n&&Dh(n,e)?e.maxv.isGreaterThan(n.maxv)&&(n.maxv=e.maxv):(i.push(e),n=e);return i}function Dh(t,e){return e.minv.block,t.maxv.block,t.maxv.block-t.minv.block<5e6}class Ph{constructor(t){this.tabix=!0}parse(t,e){const i=new Nh(new DataView(t)),n=i.getInt();if(21582659!==n)throw 38359875===n?Error("CSI version 2 is not supported. Please enter an issue at https://github.com/igvteam/igv.js"):Error("Not a CSI index");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=i.getInt(),this.depth=i.getInt();const r=[];let s=0;if(i.getInt()>=28){i.getInt(),i.getInt(),i.getInt(),i.getInt(),i.getInt(),i.getInt();const t=i.getInt(),n=i.position+t;let s=0;for(;i.positiono)i.getInt(),i.getVPointer(),i.getVPointer(),i.getLong(),i.getLong();else{e[t]=[];const n=i.getInt();for(let r=0;rs&&(s=r.block),e[t].push([n,r]))}}}r>0&&(this.indices[t]={binIndex:e,loffset:n})}this.lastBlockPosition=s}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(t,e,i){const n=this.indices[t];if(n){const t=this.reg2bins(e,i);if(0==t.length)return[];const r=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(n.binIndex[t]){const e=n.binIndex[t];for(let i of e){const e=i[0],n=i[1];r.push({minv:e,maxv:n,bin:t})}}return Oh(r,n.loffset[t[0]])}return[]}reg2bins(t,e){(t-=1)<1&&(t=1),e>2**34&&(e=2**34),e-=1;let i=0,n=0,r=this.minShift+3*this.depth;const s=[];for(;i<=this.depth;r-=3,n+=1<<3*i,i+=1){const i=n+(t>>r),o=n+(e>>r);s.push([i,o])}return s}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}class zh{constructor(){}async parse(t,e,i){const n=[];let r=Number.MAX_SAFE_INTEGER,s=0;const o=new Nh(new DataView(t)),a=o.getInt(),l={};if(!(21578050===a||e&&21578324===a))throw new Error(indexURL+" is not a "+(e?"tabix":"bai")+" file");{const t=o.getInt();if(e){o.getInt(),o.getInt(),o.getInt(),o.getInt(),o.getInt(),o.getInt(),o.getInt();for(let e=0;es&&(s=n.block),t[e].push([i,n]))}}}const l=o.getInt();for(let t=0;t0&&(n[e]={binIndex:t,linearIndex:i})}this.firstBlockPosition=r,this.lastBlockPosition=s,this.indices=n,this.sequenceIndexMap=l,this.tabix=e}}get chromosomeNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(t,e,i){const n=this.indices[t];if(n){const t=function(t,e){const i=[];return e>=1<<29&&(e=1<<29),--e,i.push([0,0]),i.push([1+(t>>26),1+(e>>26)]),i.push([9+(t>>23),9+(e>>23)]),i.push([73+(t>>20),73+(e>>20)]),i.push([585+(t>>17),585+(e>>17)]),i.push([4681+(t>>14),4681+(e>>14)]),i}(e,i),r=[];for(let e of t)for(let t=e[0];t<=e[1];t++)if(n.binIndex[t]){const e=n.binIndex[t];for(let t of e){const e=t[0],i=t[1];r.push({minv:e,maxv:i})}}const s=n.linearIndex.length;let o;const a=Math.min(e>>14,s-1),l=Math.min(i>>14,s-1);for(let t=a;t<=l;t++){const e=n.linearIndex[t];if(e){o=e;break}}return Oh(r,o)}return[]}}class Uh{constructor(){}async parse(t,e){let i=0;this.chrIndex={},this.lastBlockPosition=[];const n=new Nh(new DataView(t));!function(t){t.getInt(),t.getInt();const e=t.getInt();if(t.getString(),t.getLong(),t.getLong(),t.getString(),t.getInt(),e>=3){let e=t.getInt();for(;e-- >0;)t.getString(),t.getString()}}(n);let r=n.getInt();for(;r-- >0;){let t=n.getString();e&&(t=e.getChromosomeName(t));const r=n.getInt(),s=n.getInt(),o=n.getInt();n.getInt(),n.getInt();let a=n.getLong();const l=[];for(let t=0;ti&&(i=t)}this.chrIndex[t]={chr:t,blocks:l,longestFeature:o,binWidth:r}}this.lastBlockPosition=i}get chromosomeNames(){return Object.keys(this.chrIndex)}chunksForRange(t,e,i){const n=this.chrIndex[t];if(n){const t=n.blocks,r=n.longestFeature,s=n.binWidth,o=Math.max(e-r,0),a=Math.floor(o/s);if(a>=t.length)return[];{const e=Math.min(Math.floor((i-1)/s),t.length-1),n=t[a].min,r=t[e].max;return 0==r-n?[]:[{minv:{block:n,offset:0},maxv:{block:r,offset:0}}]}}}}async function Vh(t,e,i){let n=await zo.loadArrayBuffer(t,la(e)),r=new DataView(n);switch(31===r.getUint8(0)&&139===r.getUint8(1)&&(n=uo(n).buffer,r=new DataView(n)),r.getInt32(0,!0)){case 21578050:return async function(t,e){const i=new zh;return await i.parse(t,!1,e),i}(n,i);case 21578324:return async function(t,e){const i=new zh;return await i.parse(t,!0,e),i}(n,i);case 21582659:return async function(t,e){const i=new Ph;return i.parse(t,e),i}(n,i);case 1480870228:return async function(t,e){const i=new Uh;return i.parse(t,e),i}(n,i);case 38359875:throw Error("CSI version 2 is not supported.");default:throw Error(`Unrecognized index type: ${t}`)}}function Hh(t){return"string"==typeof t||t instanceof String?new jh(t):new $h(t)}class jh{constructor(t){this.data=t,this.ptr=0}nextLine(){var t=this.ptr,e=this.data.indexOf("\n",t),i=this.data;if(e>0)return this.ptr=e+1,e>t&&"\r"===i.charAt(e-1)?i.substring(t,e-1):i.substring(t,e);var n=i.length;return this.ptr=n,t>=n?void 0:i.substring(t)}}class $h{constructor(t){this.data=t,this.length=this.data.length,this.ptr=0}nextLine(){var t,e;if(e="",!(this.ptr>=this.length)){for(var i=this.ptr;i{const e=ArrayBuffer.isView(t)?t:new Uint8Array(t);return 1+(e[17]<<8|e[16])};class Gh{constructor(t){this.config=t,this.cacheBlocks=0!=t.cacheBlocks,this.cache=void 0}async getData(t,e){const i=t.block,n=e.block,r=0===e.offset,s=await this.getInflatedBlocks(i,n,r);if(1===s.length)return s[0];let o=0;for(const t of s)o+=t.byteLength;const a=new Uint8Array(o);let l=0;for(const t of s)a.set(t,l),l+=t.byteLength;return a}async getInflatedBlocks(t,e,i){if(this.cacheBlocks){const n=this.cache;if(n&&n.startBlock<=t&&(n.endBlock>=e||i&&n.nextEndBlock===e)){const i=t-n.startBlock,r=e-n.startBlock;return Yh(n.buffer,i,r)}{let r;if(!n||n.startBlock>e||n.endBlock=n.endBlock)o=n.buffer;else{const i=Math.max(0,t-n.startBlock);let r;if(e>=n.endBlock)r=n.buffer.byteLength;else{const t=Zh(n.buffer);for(let i=0;in.endBlock){const t=await this.loadBLockData(n.endBlock,e,{skipStart:!0,skipEnd:i});s.push(t)}r=function(t){if(1===t.length)return t[0];let e=0;for(const i of t)e+=i.byteLength;const i=new Uint8Array(e);let n=0;for(const e of t)i.set(new Uint8Array(e),n),n+=e.byteLength;return i.buffer}(s)}let s=e;if(i){const t=Zh(r);e=t[t.length-1]}return this.cache={startBlock:t,endBlock:e,nextEndBlock:s,buffer:r},Yh(r)}}return Yh(await this.loadBLockData(t,e,{skipEnd:i}))}async loadBLockData(t,e,i){const n=this.config,r=i&&i.skipStart;let s=0;if(!i||!i.skipEnd){const t=la(n,{range:{start:e,size:26}}),i=await zo.loadArrayBuffer(n.url,t);s=Wh(i)}if(r){const e=la(n,{range:{start:t,size:26}}),i=await zo.loadArrayBuffer(n.url,e);t+=Wh(i)}const o=la(n,{range:{start:t,size:e+s-t}});return zo.loadArrayBuffer(n.url,o)}}function Zh(t){const e=t.byteLength;let i=0;const n=[0];for(;it.blocks)).map((t=>t.max)).reduce(((t,e)=>Math.min(t,e)),Number.MAX_SAFE_INTEGER),n=la(this.config,{bgz:t.tabix,range:{start:0,size:i}});e=Hh(await zo.loadString(this.config.url,n))}return this.header=await this.parser.parseHeader(e),this.header}{const t=la(this.config),e=await zo.loadString(this.config.url,t);let i=Hh(e);return this.header=await this.parser.parseHeader(i),i=Hh(e),this.features=await this.parser.parseFeatures(i),this.header}}getParser(t){switch(t.format){case"vcf":return new wh(t);case"seg":return new fh("seg");case"mut":return new fh("mut");case"maf":return new fh("maf");case"gwas":return new kh(t);case"aed":return new Th(t);default:return new sh(t)}}async loadFeaturesNoIndex(){if(this.features){const t=this.features;return delete this.features,t}{const t=la(this.config),e=await zo.loadString(this.config.url,t);if(!this.header){const t=Hh(e);this.header=await this.parser.parseHeader(t)}const i=Hh(e);return await this.parser.parseFeatures(i)}}async loadFeaturesWithIndex(t,e,i){this.dataURI||this.header||await this.readHeader();const n=this.config,r=this.parser,s=this.index.tabix,o=s?this.index.sequenceIndexMap[t]:t;if(void 0===o)return[];const a=this.genome,l=this.index.chunksForRange(o,e,i);if(l&&0!==l.length){const o=[];for(let h of l){let l;if(s)l=await this._blockLoader.getData(h.minv,h.maxv);else{const t=la(n,{range:{start:h.minv.block,size:h.maxv.block-h.minv.block+1}});l=await zo.loadString(n.url,t)}const c=Hh(h.minv.offset?l.slice(h.minv.offset):l);let u=await r.parseFeatures(c);u=u.filter((t=>void 0===t._f));let d=!1;for(let n=0;ni){o.push(r);break}r.end>=e&&r.start<=i&&(d||(d=!0,n>0&&o.push(u[n-1])),o.push(r))}}return o.sort((function(t,e){return t.start-e.start})),o}return[]}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return Vh(this.config.indexURL,this.config,this.genome)}async loadFeaturesFromDataURI(){if(this.features){const t=this.features;return delete this.features,t}{const t=bo(this.dataURI);let e=Hh(t);return this.header=await this.parser.parseHeader(e),this.header instanceof String&&this.header.startsWith("##gff-version 3")&&(this.format="gff3"),e=Hh(t),this.features=await this.parser.parseFeatures(e),this.features}}}const Xh=ji;class Kh{constructor(t){this.config=t}async readFeatures(t,e,i){let n;n="function"==typeof this.config.url?this.config.url({chr:t,start:e,end:i}):this.config.url.replace("$CHR",t).replace("$START",e).replace("$END",i);let r,s=Object.assign({},this.config);void 0!==this.config.body&&("function"==typeof this.config.body?s.body=this.config.body({chr:t,start:e,end:i}):s.body=this.config.body.replace("$CHR",t).replace("$START",e).replace("$END",i));const o=await zo.load(n,s);if(o&&(r="function"==typeof this.config.parser?this.config.parser(o):Xh(o)?JSON.parse(o):o),this.config.mappings){let t=Object.keys(this.config.mappings);for(let e of r)for(let i of t)e[i]=e[this.config.mappings[i]]}return r}}const Jh=function(t,e){this.config=t,this.genome=e,this.expandQueryInterval=!1};Jh.prototype.readFeatures=function(t,e,i){const n=Math.max(0,Math.floor(e));let r=Math.ceil(i);if(this.genome){const e=this.genome.getChromosome(t);e&&r>e.bpLength&&(r=e.bpLength)}const s=this.config.url+"?db="+this.config.db+"&table="+this.config.tableName+"&chr="+t+"&start="+n+"&end="+r;return zo.loadJson(s,this.config).then((function(t){return t?(t.forEach((function(t){t.hasOwnProperty("exonStarts")&&t.hasOwnProperty("exonEnds")&&t.hasOwnProperty("exonCount")&&t.hasOwnProperty("cdsStart")&&t.hasOwnProperty("cdsEnd")&&function(t){var e,i,n,r,s,o;e=t.exonCount,i=t.exonStarts.split(","),n=t.exonEnds.split(","),r=[];for(var a=0;ao||t.cdsEnd=s&&t.cdsStart<=o&&(l.cdStart=t.cdsStart),t.cdsEnd>=s&&t.cdsEnd<=o&&(l.cdEnd=t.cdsEnd),r.push(l)}t.exons=r}(t)})),t):null}))};const tc=["Name","gene_name","gene","gene_id","alias","locus","name"];class ec{constructor(t){this.format=t.format,this.nameField=t.nameField,this.filterTypes=void 0===t.filterTypes?new Set(["chromosome"]):new Set(t.filterTypes)}combineFeatures(t,e){let i;const n=this.filterTypes;if(t=t.filter((t=>void 0===n||!n.has(t.type))),"gff3"===this.format){const e=this.combineFeaturesById(t);i=this.combineFeaturesByType(e)}else i=this.combineFeaturesByType(t);return i.sort((function(t,e){return t.start-e.start})),this.numberExons(i,e),this.nameFeatures(i),i}combineFeaturesById(t){const e=new Map,i=[];for(let n of t)if(El(n.type)||Il(n.type)||!n.id)i.push(n);else{let t=e.get(n.chr);t||(t=new Map,e.set(n.chr,t));let i=t.get(n.id);i?i.push(n):t.set(n.id,[n])}for(let t of e.values())for(let e of t.values())if(e.length>1){const t=e[0];t.exons=[];for(let i of e)t.start=Math.min(t.start,i.start),t.end=Math.max(t.end,i.end),t.exons.push({start:i.start,end:i.end});i.push(t)}else i.push(e[0]);return i}combineFeaturesByType(t){const e=t.filter((t=>"gene"===t.type||t.type.endsWith("_gene"))),i=Object.create(null);for(let t of e)i[t.id]=t;const n=Object.create(null),r=[],s=new Set,o=this.filterTypes;t=t.filter((t=>void 0===o||!o.has(t.type)));for(let e of t)if("biological_region"===e.type&&console.log(),Il(e.type)){const t=e.id;if(void 0!==t){const o=new Ll(e);n[t]=o,r.push(o),s.add(e);const a=i[e.parent];a&&(o.geneObject=a,s.add(a))}}for(let e of t)if(El(e.type)){const t=h(e);if(t)for(let i of t){let o=n[i];if(!o&&"gtf"===this.format){const t=Object.assign({},e);t.type="transcript",o=new Ll(t),n[i]=o,r.push(o)}if(void 0!==o){if(a=e.type,kl.has(a))if(t.length>1){const t=new Rl(e);o.addExon(t)}else o.addExon(e);else o.addPart(e);s.add(e)}}}var a;r.forEach((function(t){"function"==typeof t.finish&&t.finish()}));const l=t.filter((t=>!s.has(t)));for(let t of l)r.push(t);return r;function h(t){return t.parent&&""!==t.parent.trim()?t.parent.trim().split(","):null}}numberExons(t,e){for(let i of t)if(i.exons&&(!e||i.end<=e.end&&i.start>e.start))for(let t=0;t0){const t=1===this.variant_types.length?"Type":"Types";let i;for(let t of this.variant_types)i?i+=", "+t.display_name:i=t.display_name;e.push({name:t,value:i})}return e.push({name:"Actionability",value:this.actionabilityScore}),e.push({name:"Location",value:this.locationString}),e;function i(t,e){return""+t+""}}}class cc{constructor(t,e){if(this.config=t,this.genome=e,this.format=t.format?t.format.toUpperCase():"BAM","BAM"!==this.format&&"VCF"!==this.format)throw Error(`htsget format ${t.format} is not supported`)}async readHeaderData(){const t=`${uc(this.config)}?class=header&format=${this.format}`,e=await zo.loadJson(t,la(this.config));return await this.loadUrls(e.htsget.urls)}async readData(t,e,i){const n=`${uc(this.config)}?format=${this.format}&referenceName=${t}&start=${Math.floor(e)}&end=${Math.ceil(i)}`,r=await zo.loadJson(n,la(this.config));return this.loadUrls(r.htsget.urls)}async loadUrls(t){const e=[];for(let i of t)if(i.url.startsWith("data:"))e.push(Promise.resolve(dc(i.url)));else{const t=la(this.config||{});i.headers&&(t.headers=Object.assign(t.headers||{},i.headers)),e.push(zo.loadArrayBuffer(i.url,t))}return function(t){let e=0;for(let i of t)e+=i.byteLength;let i=0;const n=new Uint8Array(e);for(let e of t){const t=new Uint8Array(e);n.set(t,i),i+=t.length}return n}(await Promise.all(e))}static async inferFormat(t){try{const e=uc(t),i=`${e}${e.includes("?")?"&":"?"}class=header`,n=await zo.loadJson(i,la(t));if(n.htsget){const e=n.htsget.format;if("BAM"!==e&&"VCF"!==e)throw Error(`htsget format ${e} is not supported`);t.format=e.toLowerCase(),t.sourceType="htsget",t.name||(t.name=await ua(t.url))}}catch(t){}}}function uc(t){if(t.url&&t.endpoint&&t.id)return t.url+t.endpoint+t.id;if(t.endpoint&&t.id)return t.endpoint+t.id;if(t.url)return t.url.startsWith("htsget://")?t.url.replace("htsget://","https://"):t.url;throw Error("Must specify either 'url', or 'endpoint' and 'id")}function dc(t){const e=t.split(","),i=e[0].split(":")[1];let n=e[1];n=i.indexOf("base64")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s=i[t]){n.row=t,i[t]=n.end;break}n.row=t,i[t]=n.end}}function gc(t,e,i){const n=i||1e4,r=t=>{const i=Object.assign({},t);return i.chr="all",i.start=e.getGenomeCoordinate(t.chr,t.start),i.end=e.getGenomeCoordinate(t.chr,t.end),i._f=t,i.exons&&delete i.exons,i},s=new Set(e.wgChromosomeNames),o=[];let a=0;for(let i of e.wgChromosomeNames){if(Array.isArray(t)){const i={};for(let n of t){const t=e.getChromosomeName(n.chr);i.hasOwnProperty(t)||(i[t]=[]),i[t].push(n)}t=i}const l=t[i];if(l)for(let t of l){let i=e.getChromosomeName(t.chr);if(s.has(i))if(o.lengthi-e&&!1!==this.config.expandQuery){const t=Math.min(4.1*(i-e),n);s=Math.max(0,(e+i)/2-t),o=e+t}let a=await r.readFeatures(t,s,o);void 0===this.queryable&&(this.queryable=r.indexed);const l=this.queryable?new Da(t,s,o):void 0;a?(!1===this.config.assembleGFF||"gtf"!==this.config.format&&"gff3"!==this.config.format&&"gff"!==this.config.format||(a=new ec(this.config).combineFeatures(a,l)),"wig"!==this.config.format&&"junctions"!==this.config.type&&mc(a,this.config.maxRows||Number.MAX_SAFE_INTEGER),this.featureCache=new Zo(a,this.genome,l),this.searchable&&this.genome.addFeaturesToDB(a,this.config)):this.featureCache=new Zo([],l)}}class yc{constructor(t,e,i){this.path=t.url,this.bufferSize=i||512e3,this.range={start:-1,size:-1},this.config=t}async dataViewForRange(t,e,i=0){try{if(!(this.data&&this.range.start<=t.start&&this.range.start+this.range.size>=t.start+t.size)){let e;e=t.size?Math.max(this.bufferSize,t.size):this.bufferSize,this.contentLength&&(e=Math.min(e,this.contentLength-t.start));const i={start:t.start,size:e},n=await zo.loadArrayBuffer(this.path,la(this.config,{range:i}));this.data=n,this.range=i}const i=this.data.byteLength,n=t.start-this.range.start;return e?new Uint8Array(this.data,n,i-n):new DataView(this.data,n,i-n)}catch(n){if(0===i&&n.message&&n.message.startsWith("416")){try{return this.contentLength=await zo.getContentLength(this.path,la(this.config)),this.dataViewForRange(t,e,++i)}catch(t){console.error(t)}throw n}}}}let vc=512e3;class wc{constructor(t,e){this.path=t.url,this.format=t.format||"bigwig",this.genome=e,this.rpTreeCache={},this.config=t,this.loader=fa(this.path)?new Rc(this.path):zo}async readWGFeatures(t,e){await this.loadHeader();const i=this.chromTree.idToChrom.length-1,n=this.chromTree.idToChrom[0],r=this.chromTree.idToChrom[i];return this.readFeatures(n,0,r,Number.MAX_VALUE,t,e)}async readFeatures(t,e,i,n,r,s){await this.loadHeader();const o=this.chromTree.chromToID[t],a=this.chromTree.chromToID[i];if(void 0===o||void 0===a)return[];let l,h;if("bigwig"===this.type){const t=await this.getZoomHeaders();let e=r?function(t,e){let i;for(let n=0;n0?lo(r):r,h.call(this,new DataView(u.buffer),o,e,a,n,c,this.chromTree.idToChrom,s)}return c.sort((function(t,e){return t.start-e.start})),c}return[]}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let t,e=await this.loader.loadArrayBuffer(this.path,la(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;let i=new Nh(new DataView(e)),n=i.getUInt();if(2291137574===n)this.type="bigwig";else if(2273964779===n)this.type="bigbed";else{this.littleEndian=!1,i.littleEndian=!1,i.position=0;let t=i.getUInt();654085990===t?this.type="bigwig":3958540679===t&&(this.type="bigbed")}t={bwVersion:i.getUShort(),nZoomLevels:i.getUShort(),chromTreeOffset:i.getLong(),fullDataOffset:i.getLong(),fullIndexOffset:i.getLong(),fieldCount:i.getUShort(),definedFieldCount:i.getUShort(),autoSqlOffset:i.getLong(),totalSummaryOffset:i.getLong(),uncompressBuffSize:i.getInt(),extensionOffset:i.getLong()};const r=64;let s={start:r,size:t.fullDataOffset-r+5};e=await this.loader.loadArrayBuffer(this.path,la(this.config,{range:s}));const o=t.nZoomLevels;i=new Nh(new DataView(e)),this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let t=1;t<=o;t++){const e=o-t,n=new _c(e,i);this.firstZoomDataOffset=Math.min(n.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[e]=n}if(t.autoSqlOffset>0){i.position=t.autoSqlOffset-r;const e=i.getString();e&&(this.autoSql=function(t){let e;const i=[];let n=!1;const r=t.trim().split(/\s*[\r\n]+\s*/g);for(let t of r)if(t.startsWith("table"))e=t.split(/\s+/)[1].trim();else if(t.startsWith("("))n=!0;else if(t.startsWith(")"));else if(n&&t.length>0){const e=t.indexOf(";"),n=t.substr(0,e).split(/\s+/),r=t.substr(e+1).replace(/"/g,"").trim();i.push({type:n[0],name:n[1],description:r})}return{table:e,fields:i}}(e))}if(t.totalSummaryOffset>0&&(i.position=t.totalSummaryOffset-r,this.totalSummary=new Ac(i)),!(t.chromTreeOffset>0))throw"BigWig chromosome tree offset <= 0";return i.position=t.chromTreeOffset-r,this.chromTree=new Sc(i,r,this.genome),i.position=t.fullDataOffset-r,t.dataCount=i.getInt(),this.setDefaultVisibilityWindow(t),this.header=t,this.header}}async loadRPTree(t){let e=this.rpTreeCache[t];return e||(e=new xc(t,this.config,this.littleEndian,this.loader),await e.load(),this.rpTreeCache[t]=e,e)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),"bigwig"===this.type?"wig":this.autoSql&&"chromatinInteract"===this.autoSql.table?"interact":"annotation"}setDefaultVisibilityWindow(t){if("bigwig"===this.type)this.visibilityWindow=-1;else{let e=this.genome?this.genome.getGenomeLength():3088286401;this.visibilityWindow=t.dataCount<1e3?-1:e/t.dataCount*1e3}}}class _c{constructor(t,e){this.index=t,this.reductionLevel=e.getInt(),this.reserved=e.getInt(),this.dataOffset=e.getLong(),this.indexOffset=e.getLong()}}class xc{constructor(t,e,i,n){this.config=e,this.loader=n,this.fileOffset=t,this.path=e.url,this.littleEndian=i}async load(){const t=this.fileOffset+48,e=fa(this.path)?this.loader:new yc(this.config,vc);return this.rootNode=await this.readNode(t,e),this}async readNode(t,e){let i=await e.dataViewForRange({start:t,size:4},!1),n=new Nh(i,this.littleEndian);const r=1===n.getByte();n.getByte();const s=n.getUShort();let o={start:t+=4,size:s*(r?32:24)};i=await e.dataViewForRange(o,!1);const a=new Array(s);if(n=new Nh(i),r){for(let t=0;t=0&&(n.position=r);let o=n.getByte();n.getByte();let a,l,u,d,f,p,g=n.getUShort();if(1===o)for(a=0;at.startChrom||n===t.startChrom&&r>=t.startBase)&&(e0){this.mean=this.sumData/t,this.stddev=Math.sqrt(this.sumSquares/(t-1));let e=this.minVal<0?this.mean-2*this.stddev:0,i=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:e,max:i}}}function Ic(t,e,i,n,r,s,o){const a=new Nh(t),l=a.getInt(),h=a.getInt();let c=h,u=a.getInt();const d=a.getInt(),f=a.getInt(),p=a.getByte();a.getByte();let g=a.getUShort();if(l>=e&&l<=n){let t=0;for(;g-- >0;){let g;switch(p){case 1:c=a.getInt(),u=a.getInt(),g=a.getFloat();break;case 2:c=a.getInt(),g=a.getFloat(),u=c+f;break;case 3:g=a.getFloat(),c=h+t*d,u=c+f,t++}if(!(ln||l===n&&c>=r)break;if(Number.isFinite(g)){const t=o[l];s.push({chr:t,start:c,end:u,value:g})}}}}}function Ec(){const t=function(t,e,i,n){if("biginteract"===n||i&&"chromatinInteract"===i.table||"interact"===i.table)return function(t,e){return t.chr1=e[5],t.start1=Number.parseInt(e[6]),t.end1=Number.parseInt(e[7]),t.chr2=e[10],t.start2=Number.parseInt(e[11]),t.end2=Number.parseInt(e[12]),t.name=e[0],t.score=Number(e[1]),t.value=Number(e[2]),t.color="."===e[4]?void 0:"0"===e[4]?"rgb(0,0,0)":e[4],t};{const n=t-3;return function(r,s){if(n>0&&(r.name=s[0]),n>1&&(r.score=Number(s[1])),n>2&&(r.strand=s[2]),n>3&&(r.cdStart=parseInt(s[3])),n>4&&(r.cdEnd=parseInt(s[4])),n>5&&"."!==s[5]&&"0"!==s[5]&&"-1"!==s[5]){const t=xo.createColorString(s[5]);r.color=t.startsWith("rgb")?t:void 0}if(n>8){const t=parseInt(s[6]),e=s[7].split(","),i=s[8].split(","),n=[];for(let s=0;si?n.utr=!0:(e>=r&&e<=t&&(n.cdStart=e),i>=r&&i<=t&&(n.cdEnd=i))}}(n,r.cdStart,r.cdEnd),r.exons=n}if(i)for(let n=t;n=13;){const e=l.getInt(),h=a[e],c=l.getInt(),u=l.getInt(),d=l.getString();if(!(er||e===r&&c>=s)break;if(u>0){const e={chr:h,start:c,end:u};o.push(e);const i=d.split("\t");t(e,i)}}}}}function Mc(t,e,i,n,r,s,o,a){const l=new Nh(t);for(;l.remLength()>=32;){const t=l.getInt(),h=o[t],c=l.getInt(),u=l.getInt(),d=l.getInt(),f=l.getFloat(),p=l.getFloat(),g=l.getFloat();let m;switch(l.getFloat(),a){case"min":m=f;break;case"max":m=p;break;default:m=0===d?0:g/d}if(!(tn||t===n&&c>=r)break;Number.isFinite(m)&&s.push({chr:h,start:c,end:u,value:m})}}}class Rc{constructor(t){this.data=bo(t).buffer}loadArrayBuffer(t,e){const i=e.range;return i?this.data.slice(i.start,i.start+i.size):this.data}async dataViewForRange(t,e){const i=Math.min(this.data.byteLength-t.start,t.size);return e?new Uint8Array(this.data,t.start,i):new DataView(this.data,t.start,i)}}class Lc{constructor(t,e){this.reader=new wc(t,e),this.genome=e,this.format=t.format||"bigwig",this.wgValues={},this.queryable=!0}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n,windowFunction:r}){const s="bigwig"===this.reader.type,o="all"===t.toLowerCase()?s?await this.getWGValues(r):[]:await this.reader.readFeatures(t,e,t,i,n,r);return s||pc(o),o}async getHeader(){return this.reader.loadHeader()}getDefaultRange(){return void 0!==this.reader.totalSummary?this.reader.totalSummary.defaultRange:void 0}async defaultVisibilityWindow(){return this.reader.defaultVisibilityWindow}async getWGValues(t){const e=this.genome;if(this.wgValues[t])return this.wgValues[t];{const i=e.getGenomeLength()/1e3,n=await this.reader.readWGFeatures(i,t);let r=[];for(let t of n){const i=t.chr,n=e.getCumulativeOffset(i),s=Object.assign({},t);s.chr="all",s.start=n+t.start,s.end=n+t.end,r.push(s)}return this.wgValues[t]=r,r}}supportsWholeGenome(){return"bigwig"===this.reader.type}async trackType(){return this.reader.getTrackType()}}class Bc{constructor(t,e){this.config=t,this.genome=e,this.path=t.url,this.groupCache={},this.datasetCache={}}async readHeader(){if(void 0!==this.magic)return this;let t=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:0,size:64e3}})),e=new Nh(new DataView(t));if(this.magic=e.getInt(),this.version=e.getInt(),this.indexPos=e.getLong(),this.indexSize=e.getInt(),e.getInt(),this.version>=2){let t=e.getInt();for(this.windowFunctions=[];t-- >0;)this.windowFunctions.push(e.getString())}this.trackType=e.getString(),this.trackLine=e.getString();let i=e.getInt();for(this.trackNames=[];i-- >0;)this.trackNames.push(e.getString());this.genomeID=e.getString(),this.flags=e.getInt(),this.compressed=0!=(1&this.flags),t=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:this.indexPos,size:this.indexSize}})),e=new Nh(new DataView(t)),this.datasetIndex={};let n=e.getInt();for(;n-- >0;){const t=e.getString(),i=e.getLong(),n=e.getInt();this.datasetIndex[t]={position:i,size:n}}for(this.groupIndex={},n=e.getInt();n-- >0;){const t=e.getString(),i=e.getLong(),n=e.getInt();this.groupIndex[t]={position:i,size:n}}return this}async readDataset(t,e,i){const n=t+"_"+e+"_"+i;if(this.datasetCache[n])return this.datasetCache[n];{await this.readHeader();const r=this.version<2?"":"/"+e,s="all"===t.toLowerCase()||void 0===i?"0":i.toString();let o;o="raw"===e?"/"+t+"/raw":"/"+t+"/z"+s+r;const a=this.datasetIndex[o];if(void 0===a)return;const l=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:a.position,size:a.size}}));if(!l)return;const h=new Nh(new DataView(l));let c=h.getInt();const u={};for(;c-- >0;)u[h.getString()]=h.getString();const d=h.getString(),f=h.getFloat();let p=h.getInt();const g=[];for(;p-- >0;)g.push({position:h.getLong(),size:h.getInt()});const m={name:o,attributes:u,dataType:d,tileWidth:f,tiles:g};return this.datasetCache[n]=m,m}}async readRootGroup(){const t=this.genome,e=this.groupCache["/"];if(e)return e;{const e=await this.readGroup("/"),i=e.chromosomes,n=e.maxZoom;n&&(this.maxZoom=Number(n));const r=e.totalCount;r&&(e.totalCount=Number(r));const s={};return i&&i.split(",").forEach((function(e){const i=t.getChromosomeName(e);s[i]=e})),this.chrAliasTable=s,this.groupCache["/"]=e,e}}async readGroup(t){const e=this.groupCache[t];if(e)return e;{await this.readHeader();const e=this.groupIndex[t];if(void 0===e)return;const i=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:e.position,size:e.size}}));if(!i)return;const n=new Nh(new DataView(i)),r={name:t};let s=n.getInt();for(;s-- >0;){const t=n.getString(),e=n.getString();r[t]=e}return this.groupCache[t]=r,r}}async readTiles(t,e){if(t.sort((function(t,e){return t.position-e.position})),0===(t=t.filter((function(t){return t.size>0}))).length)return Promise.resolve([]);const i=t[0],n=t[t.length-1],r=i.position,s=n.position+n.size-r,o=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:r,size:s}})),a=[];for(let i of t){const t=i.position-r,n=i.size;if(n>0){let i;i=this.compressed?lo(o.slice(t,t+n)).buffer:o.slice(t,t+n);const r=new Nh(new DataView(i)),s=r.getString();let l;switch(s){case"fixedStep":l=Nc(r,e);break;case"variableStep":l=Fc(r,e);break;case"bed":case"bedWithName":l=Oc(r,e,s);break;default:throw"Unknown tile type: "+s}a.push(l)}}return a}async readTile(t,e){let i=await zo.loadArrayBuffer(this.path,la(this.config,{range:{start:t.position,size:t.size}}));this.compressed&&(i=lo(i).buffer);const n=new Nh(new DataView(i)),r=n.getString();switch(r){case"fixedStep":return Nc(n,e);case"variableStep":return Fc(n,e);case"bed":case"bedWithName":return Oc(n,e,r);default:throw"Unknown tile type: "+r}}}function Nc(t,e){const i=t.getInt(),n=t.getInt(),r=t.getFloat(),s=[];let o=e;for(;o-- >0;){let e=i;const n=[];for(;e-- >0;)n.push(t.getFloat());s.push(n)}return{type:"fixedStep",start:n,span:r,data:s,nTracks:e,nPositions:i}}function Fc(t,e){const i=t.getInt(),n=t.getFloat(),r=t.getInt(),s=[];let o=r;for(;o-- >0;)s.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){o=r;const e=[];for(;o-- >0;)e.push(t.getFloat());a.push(e)}return{type:"variableStep",tileStart:i,span:n,start:s,data:a,nTracks:e,nPositions:r}}function Oc(t,e,i){const n=t.getInt();let r=n;const s=[];for(;r-- >0;)s.push(t.getInt());r=n;const o=[];for(;r-- >0;)o.push(t.getInt());t.getInt();const a=[];let l=e;for(;l-- >0;){let e=n;const i=[];for(;e-- >0;)i.push(t.getFloat());a.push(i)}if("bedWithName"===i){r=n;const e=[];for(;r-- >0;)e.push(t.getString())}return{type:i,start:s,end:o,data:a,nTracks:e,nPositions:n}}class Dc{constructor(t,e){this.genome=e,this.windowFunction=t.windowFunction||"mean",this.reader=new Bc(t,e),this.queryable=!0}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n}){if("all"===t.toLowerCase()){const t=[],e=this.genome;if(this.genome.wgChromosomeNames)for(let i of e.wgChromosomeNames){const r=e.getChromosome(i).bpLength;n=r/1e3;const s=await this._getFeatures(i,0,r,n);if(s)for(let i of s){const n=Object.assign({},i);n.chr="all",n.start=e.getGenomeCoordinate(i.chr,i.start),n.end=e.getGenomeCoordinate(i.chr,i.end),n._f=i,t.push(n)}}return t}return this._getFeatures(t,e,i,n)}async _getFeatures(t,e,i,n){const r=new Da(t,e,i),s=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const t=this.rootGroup.totalCount;t&&(this.normalizationFactor=1e6/t)}r.bpPerPixel=n;const o=function(t,e,i){var n=i.getChromosome(t).bpLength;return Math.ceil(Math.log(Math.max(0,n/(700*e)))/Vc)}(t,n,s);let a=this.reader.chrAliasTable[t],l=this.reader.maxZoom;void 0===a&&(a=t),void 0===l&&(l=-1);const h=o>l?"raw":this.windowFunction,c=await this.reader.readDataset(a,h,o);if(null==c)return[];const u=c.tileWidth,d=Math.floor(e/u),f=Math.floor(i/u),p=await this.reader.readTiles(c.tiles.slice(d,f+1),1),g=[];for(let n of p)switch(n.type){case"bed":Pc(n,t,e,i,0,g);break;case"variableStep":zc(n,t,e,i,0,g);break;case"fixedStep":Uc(n,t,e,i,0,g);break;default:throw"Unknown tile type: "+n.type}return g.sort((function(t,e){return t.start-e.start})),g}get supportsWholeGenome(){return!0}}function Pc(t,e,i,n,r,s){const o=t.nPositions,a=t.start,l=t.end,h=t.data[0];for(let t=0;tn)break;s.push({chr:e,start:r,end:o,value:h[t]})}}}function zc(t,e,i,n,r,s){const o=t.nPositions,a=t.start,l=t.span,h=t.data[0];for(let t=0;tn)break;s.push({chr:e,start:r,end:o,value:h[t]})}}}function Uc(t,e,i,n,r,s){const o=t.nPositions;let a=t.start;const l=t.span,h=t.data[0];for(let t=0;tn)break;r>=i&&(Number.isNaN(h[t])||s.push({chr:e,start:a,end:r,value:h[t]})),a=r}}var Vc=Math.log(2);class Hc{constructor(t,e){this.config=t,this.genome=e,this.queryable=!1,this.searchable=!1!==t.searchable,this.updateFeatures(t.features)}updateFeatures(t){mc(t=function(t,e){if(e)for(let i of t)i.chr=e.getChromosomeName(i.chr);return t}(t,this.genome)),this.config.mappings&&function(t,e){let i=Object.keys(e);t.forEach((function(t){i.forEach((function(i){t[i]=t[e[i]]}))}))}(t,this.config.mappings),this.featureCache=new Zo(t,this.genome),(this.searchable||this.config.searchableFields)&&this.genome.addFeaturesToDB(t,this.config)}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome,o=s?s.getChromosomeName(t):t;return"all"===o.toLowerCase()?gc(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(o,e,i)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}}const jc=new Set(["bigwig","bw","bigbed","bb","biginteract","biggenepred","bignarrowpeak"]);function $c(t,e){const i=t.format?t.format.toLowerCase():void 0;return t.features?new Hc(t,e):jc.has(i)?new Lc(t,e):"tdf"===i?new Dc(t,e):new bc(t,e)}const qc=function(t,e){const{r:i,g:n,b:r}=Ko.nickel;return`rgba(${i},${n},${r},0.125)`}(),Wc=qc;class Gc{constructor(t,e){if(this.url=t.url,t.name?this.name=t.name:t.url&&Yi(t.url)?this.name=t.url.name:t.url&&ji(t.url)&&!t.url.startsWith("data:")&&(this.name=Zi(t.url)),this.isUserDefined=t.isUserDefined,t.features)this.featureSource=new Yc(t.features,e);else{if(t.format)t.format=t.format.toLowerCase();else{const e=Zi(t.url);t.format=ka(e)}this.featureSource=t.featureSource||$c(t,e)}!0===this.isUserDefined?(this.color=t.color||Wc,this.headerColor="rgba(155,185,129)"):(this.color=t.color||qc,this.headerColor="rgb(190,190,190)")}async getFeatures(t,e,i){return this.featureSource.getFeatures({chr:t,start:e,end:i})}async getAllFeatures(){return"function"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(t){this.isUserDefined?this.featureSource.addFeature(t):console.error("Attempt to add ROI to non user-defined set")}removeFeature(t){this.isUserDefined?this.featureSource.removeFeature(t):console.error("Attempt to remove ROI from non user-defined set")}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined};{const t=this.featureSource.getAllFeatures(),e=[];for(let i of Object.keys(t))for(let n of t[i])e.push(n);return{name:this.name,color:this.color,features:e,isUserDefined:this.isUserDefined}}}dispose(){for(let t of Object.keys(this))this[t]=void 0}}function Zc(t,e,i,n){let r=Math.round((t-i)/n),s=Math.round((e-i)/n)-r;return s<3&&(s=3,r-=1),{x:r,width:s}}class Yc{constructor(t,e){this.featureMap={},this.genome=e;for(let i of t){const t=e?e.getChromosomeName(i.chr):i.chr;let n=this.featureMap[t];n||(n=[],this.featureMap[t]=n),n.push(i)}for(let t of Object.keys(this.featureMap))this.featureMap[t].sort(((t,e)=>t.start-e.start))}getFeatures({chr:t,start:e,end:i}){if("all"===t.toLowerCase())return gc(this.featureMap,this.genome);{const n=this.featureMap[t];return n?n.filter((t=>t.end>e&&t.startt.start-e.start))}removeFeature({chr:t,start:e,end:i}){if(this.featureMap[t]){const n=`${t}-${e}-${i}`;this.featureMap[t]=this.featureMap[t].filter((t=>n!==`${t.chr}-${t.start}-${t.end}`))}}}class Qc{constructor(t,e,i,n){this.rulerViewport=t,this.rulerSweeper=_e.div({class:"igv-ruler-sweeper"}),e.appendChild(this.rulerSweeper),this.browser=i,this.referenceFrame=n,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(ul.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on("locuschange",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off("locuschange",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let t,e,i,n,r,s;this.boundContentMouseDownHandler=function(s){t=!0,e=!0;const{x:o}=_e.translateMouseCoordinates(s,this.rulerViewport.contentDiv);n=i=o,r=1,this.rulerSweeper.style.display="block",this.rulerSweeper.style.backgroundColor=!0===s.shiftKey?Wc:"rgba(68, 134, 247, 0.25)",this.rulerSweeper.style.left=`${n}px`,this.rulerSweeper.style.width=`${r}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener("mousedown",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(o){let a;if(t&&e){const{x:t}=_e.translateMouseCoordinates(o,this.rulerViewport.contentDiv);a=Math.max(Math.min(t,this.rulerViewport.contentDiv.clientWidth),0),s=a-i,r=Math.abs(s),this.rulerSweeper.style.width=`${r}px`,s<0&&(n=i+s,this.rulerSweeper.style.left=`${n}px`)}}.bind(this),document.addEventListener("mousemove",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(i){let s;!0===t&&!0===e&&(t=e=void 0,this.rulerSweeper.style.display="none",r>1)&&(s={start:Math.floor(this.referenceFrame.calculateEnd(n)),end:Math.floor(this.referenceFrame.calculateEnd(n+r))},!0===i.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},s)):(ca(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,s,this.browser.minimumBases()),function(t,e,i){t.start=Math.round(e.start),t.end=Math.round(e.end),t.bpPerPixel=(t.end-t.start)/i}(this.referenceFrame,s,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame)))}.bind(this),document.addEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener("mousedown",this.boundContentMouseDownHandler),document.removeEventListener("mousemove",this.boundDocumentMouseMoveHandler),document.removeEventListener("mouseup",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}class Xc{constructor(t){this.paired=!0,this.firstAlignment=t,this.chr=t.chr,this.readName=t.readName,t.starte.start?this.connectingEnd=t.start:this.connectingStart=t.start+t.lengthOnRef,this.start=Math.min(e.start,t.start),this.end=Math.max(e.start+e.lengthOnRef,t.start+t.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(e.scStart,t.scStart);const i=Math.max(e.scStart+e.scLengthOnRef,t.scStart+t.scLengthOnRef);this.scLengthOnRef=i-this.scStart}containsLocation(t,e){const i=e?this.scStart:this.start,n=e?this.scLengthOnRef:this.lengthOnRef;return t>=i&&t<=i+n}alignmentContaining(t,e){return this.firstAlignment.containsLocation(t,e)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(t,e)?this.secondAlignment:void 0}popupData(t){let e=this.firstAlignment.popupData(t);return this.secondAlignment&&(e.push("-------------------------------"),e=e.concat(this.secondAlignment.popupData(t))),e}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}firstOfPairStrand(){return this.firstAlignment.isFirstOfPair()?this.firstAlignment.strand:this.secondAlignment&&this.secondAlignment.isFirstOfPair()?this.secondAlignment.strand:this.firstAlignment.mate.strand}hasTag(t){return this.firstAlignment.hasTag(t)||this.secondAlignment&&this.secondAlignment.hasTag(t)}}class Kc{constructor(){this.alignments=[],this.score=void 0}findAlignment(t){const e=(t,e)=>e>=t.start&&e=r.start&&t0?c-=t:0===c&&(c=1)}return c}(r,n,t);case"STRAND":return r.strand?1:-1;case"START":return r.start;case"TAG":return r.tags()[i];case"READ_NAME":return r.readName;case"INSERT_SIZE":return-Math.abs(r.fragmentLength);case"GAP_SIZE":return-r.gapSizeAt(t);case"MATE_CHR":return r.mate;case"MQ":return void 0===r.mq?Number.MAX_VALUE:-r.mq;case"ALIGNED_READ_LENGTH":return-r.lengthOnRef;default:return Number.MAX_VALUE}}}function Jc(t){return t.isPaired()&&t.mate&&t.isMateMapped()&&t.chr===t.mate.chr&&(t.isFirstOfPair()||t.isSecondOfPair())&&!(t.isSecondary()||t.isSupplementary())}function tu(t){const e=[];for(let i of t)for(let t of i.alignments)t instanceof Xc?(t.firstAlignment&&e.push(t.firstAlignment),t.secondAlignment&&e.push(t.secondAlignment)):e.push(t);return e}function eu(t,e,i,n){if(t){if(0===t.length)return[];{t.sort((function(t,e){return n?t.scStart-e.scStart:t.start-e.start}));const e=[];let i,r=0,s=0;const o=new Set,a=()=>{i=new Kc,e.push(i),r=0,s=0,o.clear()};for(a();t.length>0;)if(s>=0&&s(n?t.scStart:t.start)>r),s)}else t=t.filter((t=>!o.has(t))),a();return e}}}function iu(t,e,i){let n=i-1,r=t.length;for(;1+n>1);e(t[i])?r=i:n=i}return r}class nu{constructor(t,e,i,{samplingWindowSize:n,samplingDepth:r,pairsSupported:s,alleleFreqThreshold:o}){this.chr=t,this.start=Math.floor(e),this.end=Math.ceil(i),this.length=i-e,this.alleleFreqThreshold=void 0===o?.2:o,this.coverageMap=new su(t,e,i,this.alleleFreqThreshold),this.alignments=[],this.downsampledIntervals=[],this.samplingWindowSize=void 0===n?100:n,this.samplingDepth=void 0===r?1e3:r,this.pairsSupported=void 0===s||s,this.paired=!1,this.pairsCache={},this.downsampledReads=new Set,this.currentBucket=new ru(this.start,this.start+this.samplingWindowSize,this),this.filter=function(t){return t.isMapped()&&!t.isFailsVendorQualityCheck()}}push(t){!1!==this.filter(t)&&(this.coverageMap.incCounts(t),this.pairsSupported&&this.downsampledReads.has(t.readName)||(t.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new ru(t.start,t.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(t)))}forEach(t){this.alignments.forEach(t)}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.alignments.sort((function(t,e){return t.start-e.start})),this.pairsCache=void 0,this.downsampledReads=void 0}contains(t,e,i){return this.chr===t&&this.start<=e&&this.end>=i}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new au(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount)),this.paired=this.paired||this.currentBucket.paired}setViewAsPairs(t){let e;e=t?function(t){const e={},i=[];for(let n of t)for(let t of n.alignments)if(Jc(t)){let n=e[t.readName];n?(n.setSecondAlignment(t),e[t.readName]=void 0):(n=new Xc(t),e[t.readName]=n,i.push(n))}else i.push(t);return i}(this.packedAlignmentRows):tu(this.packedAlignmentRows),this.packedAlignmentRows=eu(e,this.start,this.end)}setShowSoftClips(t){const e=this.allAlignments();this.packedAlignmentRows=eu(e,this.start,this.end,t)}repack(t,e){const i=this.allAlignments();this.packedAlignmentRows=eu(i,this.start,this.end,e)}allAlignments(){const t=[];for(let e of this.packedAlignmentRows)for(let i of e.alignments)t.push(i);return t}getMax(t,e){return this.coverageMap.getMax(t,e)}sortRows(t){const e=[],i=[];for(let n of this.packedAlignmentRows)void 0!==n.findAlignment(t.position)?e.push(n):i.push(n);e.sort(((e,i)=>{const n=t.direction,r=e.getSortValue(t,this),s=i.getSortValue(t,this);if(void 0===s&&void 0!==s)return 1;if(void 0!==r&&void 0===s)return-1;const o=r>s?1:re)break;const s=this.coverage[r];n>=t&&s&&(i=Math.max(i,s.total))}return i}incCounts(t){var e=this;if(void 0===t.blocks?i(t):t.blocks.forEach((function(t){i(t)})),t.gaps)for(let i of t.gaps)if("D"===i.type){const t=i.start-e.bpStart;for(let n=t;n=e}}class au{constructor(t,e,i){this.start=t,this.end=e,this.counts=i}popupData(t){return[{name:"start",value:this.start+1},{name:"end",value:this.end},{name:"# downsampled:",value:this.counts}]}}class lu{constructor(t){const e=t.split(",");this.chr=e[0],this.start=parseInt(e[1]),this.strand=e[2].charAt(0),this.mapQ=parseInt(e[4]),this.numMismatches=parseInt(e[5]),this.lenOnRef=Cu.computeLengthOnReference(e[3])}printString(){return this.chr+":"+$i(this.start)+"-"+$i(this.start+this.lenOnRef)+" ("+this.strand+") = "+$i(this.lenOnRef)+"bp @MAPQ: "+this.mapQ+" NM: "+this.numMismatches}}function hu(t){return t.split(";").filter((t=>t.length>0)).map((t=>new lu(t)))}const cu={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class uu{constructor(){this.hidden=!1}isMapped(){return 0==(4&this.flags)}isPaired(){return 0!=(1&this.flags)}isProperPair(){return 0!=(2&this.flags)}isFirstOfPair(){return 0!=(64&this.flags)}isSecondOfPair(){return 0!=(128&this.flags)}isSecondary(){return 0!=(256&this.flags)}isSupplementary(){return 0!=(2048&this.flags)}isFailsVendorQualityCheck(){return 0!=(512&this.flags)}isDuplicate(){return 0!=(1024&this.flags)}isMateMapped(){return 0==(8&this.flags)}isNegativeStrand(){return 0!=(16&this.flags)}isMateNegativeStrand(){return 0!=(32&this.flags)}hasTag(t){return(this.tagDict||fu(this.tagBA)).hasOwnProperty(t)}tags(){return this.tagDict||(this.tagBA?(this.tagDict=fu(this.tagBA),this.tagBA=void 0):this.tagDict={}),this.tagDict}containsLocation(t,e){const i=e?this.scStart:this.start,n=e?this.scLengthOnRef:this.lengthOnRef;return t>=i&&t<=i+n}popupData(t){const e=[];if(t=Math.floor(t),this.insertions){const n=this.seq;for(let r of this.insertions){var i=r.start;if(t===i||t===i-1)return e.push({name:"Insertion",value:n.substr(r.seqOffset,r.len)}),e.push({name:"Location",value:i}),e}}e.push({name:"Read Name",value:this.readName}),e.push("
"),e.push({name:"Alignment Start",value:$i(1+this.start),borderTop:!0}),e.push({name:"Read Strand",value:!0===this.strand?"(+)":"(-)",borderTop:!0});let n=this.cigar;if(n&&n.length>50){const t=25;n=`${n.substring(0,t-2)} ... ${n.substring(n.length-t+2)}`}e.push({name:"Cigar",value:n}),e.push({name:"Mapping Quality",value:this.mq}),e.push({name:"Secondary",value:o(this.isSecondary())}),e.push({name:"Supplementary",value:o(this.isSupplementary())}),e.push({name:"Duplicate",value:o(this.isDuplicate())}),e.push({name:"Failed QC",value:o(this.isFailsVendorQualityCheck())}),this.isPaired()&&(e.push("
"),e.push({name:"First in Pair",value:!this.isSecondOfPair(),borderTop:!0}),e.push({name:"Mate is Mapped",value:o(this.isMateMapped())}),this.pairOrientation&&e.push({name:"Pair Orientation",value:this.pairOrientation}),this.isMateMapped()&&(e.push({name:"Mate Chromosome",value:this.mate.chr}),e.push({name:"Mate Start",value:this.mate.position+1}),e.push({name:"Mate Strand",value:!0===this.mate.strand?"(+)":"(-)"}),e.push({name:"Insert Size",value:this.fragmentLength})));const r=this.tags();if(r.hasOwnProperty("SA")){e.push("
"),e.push({name:"Supplementary Alignments",value:""});const t=hu(r.SA);if(t){e.push("
    ");for(let i of t)e.push(`
  • ${i.printString()}
  • `);e.push("
")}}const s=new Set(["SA","MD"]);e.push("
");for(let t in r)s.has(t)||e.push({name:t,value:r[t]});return e.push({name:"Hidden Tags",value:"SA, MD"}),e.push("
"),e.push({name:"Genomic Location: ",value:$i(1+t)}),e.push({name:"Read Base:",value:this.readBaseAt(t)}),e.push({name:"Base Quality:",value:this.readBaseQualityAt(t)}),e;function o(t){return t?"Yes":"No"}}readBaseAt(t){const e=du(this.blocks,t);if(e){if("*"===this.seq)return"*";{const i=e.seqIndexAt(t);return this.seq[i]}}}readBaseQualityAt(t){const e=du(this.blocks,t);if(e){if("*"===this.qual)return 30;{const i=e.seqIndexAt(t);return i>=0&&this.qual&&i=e.start&&t=n.start&&e>1)+n;a+4=e)return!1;if("B"!==String.fromCharCode(t[a+2])||"I"!==String.fromCharCode(t[a+3]))return!1;var h=Tu(t,a+4),c=a+8;if(c+4*h>e)return!1;var u="",d=0;s.length=0,a=c;for(var f=0;f>4,m=xu[15&p];"M"!==m&&"EQ"!==m&&"X"!==m&&"D"!==m&&"N"!==m&&"="!==m||(d+=g),u=u+g+m,s.push({len:g,ltr:m})}return r.cigar=u,r.lengthOnRef=d,!0},decodeBamRecords:function(t,e,i,n,r,s,o,a){for(;et.length)return;if(p<0){e=d;continue}if(void 0!==r&&(p>r||g>o))return!0;if(void 0!==r&&p>8,y=255&m,v=Tu(t,e+16),w=(4294901760&v)>>16,_=65535&v,x=Tu(t,e+20),k=Tu(t,e+24),S=Tu(t,e+28),C=Tu(t,e+32);let A=[];for(let i=0;i>4,c=xu[15&l];"M"!==c&&"EQ"!==c&&"X"!==c&&"D"!==c&&"N"!==c&&"="!==c||(T+=h),I=I+h+c,E+=4,R={len:h,ltr:c},M.push(R)}if(f.chr=n[p],f.start=g,f.flags=w,f.strand=!(16&w),f.readName=A,f.cigar=I,f.lengthOnRef=T,f.fragmentLength=C,f.mq=b,Cu.bam_tag2cigar(t,d,E,x,f,M),f.end=f.start+f.lengthOnRef,f.end>1;for(let e=0;e>4]),L.push(_u[15&u])}L=L.slice(0,x).join(""),E+=B;const N=[];for(let e=0;e=0&&(f.mate={chr:n[k],position:S,strand:!(32&w)}),f.seq=L,f.qual=N,f.tagBA=new Uint8Array(t.buffer.slice(E,d)),this.setPairOrientation(f),(void 0===a||a.pass(f))&&(Au(f,M),i.push(f)),e=d}},decodeSamRecords:function(t,e,i,n,r,s){var o,a,l,h,c,u,d,f,p,g;for(h=(o=qi(t)).length,a=0;ar)break;if(f=0,(g=Iu(p.cigar)).forEach((function(t){var e=t.len,i=t.ltr;"M"!==i&&"EQ"!==i&&"X"!==i&&"D"!==i&&"N"!==i&&"="!==i||(f+=e)})),p.lengthOnRef=f,!(p.start+fSu&&(console.log("Warning: attempt to set sampling depth > maximum value of "+Su),t.samplingDepth=Su),e.viewAsPairs?t.pairsSupported=!0:t.pairsSupported=void 0===e.pairsSupported||e.pairsSupported},setPairOrientation:function(t){if(t.isMapped()&&t.mate&&t.isMateMapped()&&t.mate.chr===t.chr){var e=t.strand?"F":"R",i=t.mate,n=i.strand?"F":"R",r=" ",s=" ";t.isFirstOfPair()?(r="1",s="2"):t.isSecondOfPair()&&(r="2",s="1");var o=[],a=t.fragmentLength,l=t.end-t.start;0===a&&(a=(t.start0?(o[0]=e,o[1]=r,o[2]=n,o[3]=s):(o[2]=e,o[3]=r,o[0]=n,o[1]=s),t.pairOrientation=o.join("")}},computeLengthOnReference:function(t){let e=0,i="";for(let n=0;n47&&r<58)i+=t.charAt(n);else{switch(r){case 78:case 68:case 77:case 61:case 88:e+=parseInt(i.toString())}i=""}}return e}};function Au(t,e){const i=[];let n,r,s=0,o=t.start;t.scStart=t.start,t.scLengthOnRef=t.lengthOnRef;for(let a of e){let e;switch(a.ltr){case"H":case"P":break;case"S":e=o,t.scLengthOnRef+=a.len,0===i.length&&(t.scStart-=a.len,e-=a.len),i.push(new vu({start:e,seqOffset:s,len:a.len,type:"S"})),s+=a.len;break;case"N":case"D":void 0===r&&(r=[]),r.push({start:o,len:a.len,type:a.ltr}),o+=a.len;break;case"I":void 0===n&&(n=[]),n.push(new vu({start:o,len:a.len,seqOffset:s,type:"I"})),s+=a.len;break;case"M":case"EQ":case"=":case"X":i.push(new vu({start:o,seqOffset:s,len:a.len,type:"M"})),s+=a.len,o+=a.len;break;default:console.log("Error processing cigar element: "+a.len+a.ltr)}}t.blocks=i,t.insertions=n,t.gaps=r}function Tu(t,e){return t[e+3]<<24|t[e+2]<<16|t[e+1]<<8|t[e]}function Iu(t){var e,i,n,r,s,o,a,l,h;for(e=[],i=[],s=null,r=t.length,n=0;n=48&&h<=57?i.push(o):(a=o,l=Number.parseInt(i.join("")),i=[],null!==s&&s.ltr===a?s.len+=l:(s={len:l,ltr:a},e.push(s)));return e}function Eu(t){var e={};return t.forEach((function(t){var i=t.split(":");e[i[0]]=i[2]})),e}class Mu{constructor(t,e){this.config=t,this.genome=e,this.bamPath=t.url,this.isDataUri=fa(t.url),Cu.setReaderDefaults(this,t)}async readAlignments(t,e,i){if(this.alignmentCache){const n=this.header,r=n.chrAliasTable.hasOwnProperty(t)?n.chrAliasTable[t]:t,s=this.alignmentCache.queryFeatures(r,e,i),o=new nu(t,e,i,this.config);for(let t of s)o.push(t);return o.finish(),o}if(this.isDataUri){const n=uo(function(t){const e=t.split(","),i=e[0].split(":")[1];let n=e[1];n=i.indexOf("base64")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s{var t={368:function(t,e,i){var n=this&&this.__awaiter||function(t,e,i,n){return new(i||(i=Promise))((function(r,s){function o(t){try{l(n.next(t))}catch(t){s(t)}}function a(t){try{l(n.throw(t))}catch(t){s(t)}}function l(t){var e;t.done?r(t.value):(e=t.value,e instanceof i?e:new i((function(t){t(e)}))).then(o,a)}l((n=n.apply(t,e||[])).next())}))},r=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const s=r(i(4105)),o=r(i(1269)),a=i(597),l=i(3427),h=i(8577);function c(t,e){if(e.some((t=>void 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n&&i.push(Number.parseInt(n,10)),6===i.length&&c(t,i),Object.entries(t).forEach((([e,i])=>{t[e]=i.sort(((t,e)=>t.start-e.start||t.span-e.span))})),t}))}getIndex(t={}){return this._parseCache.get("index",null,t.signal)}hasDataForReferenceSequence(t){return n(this,void 0,void 0,(function*(){return!!(yield this.getIndex())[t]}))}getEntriesForRange(t,e,i){return n(this,void 0,void 0,(function*(){const n=(yield this.getIndex())[t];if(!n)return[];const r=t=>{const n=t.start,r=t.start+t.span;return n>i?-1:r<=e?1:0},s=[];for(let t=0;t{Object.defineProperty(e,"__esModule",{value:!0}),e.default=class{constructor(t,e){this.parameters=t,this.dataType=e}}},4863:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=i(8577),s=n(i(1050)),o=i(1074);class a extends s.default{constructor(t,e){if(super(t,e),"int"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet 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r=1;for(;0===(0,o.getBits)(e.content,n.coreBlock,1);)r+=1;return((0,o.getBits)(e.content,n.coreBlock,r-1)|1<{Object.defineProperty(e,"__esModule",{value:!0}),e.getBits=e.CramBufferOverrunError=void 0;class i extends Error{}e.CramBufferOverrunError=i,e.getBits=function(t,e,n){let r=0;if(e.bytePosition+(7-e.bitPosition+n)/8>t.length)throw new i("read error during decoding. the file seems to be truncated.");for(let i=n;i;i--)r<<=1,r|=t[e.bytePosition]>>e.bitPosition&1,e.bitPosition-=1,e.bitPosition<0&&(e.bytePosition+=1),e.bitPosition&=7;return r}},2082:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=i(8577),s=n(i(1050)),o=i(1074);class a extends s.default{constructor(t,e){if(super(t,e),this.codes={},this.codeBook={},this.sortedByValue=[],this.sortedCodes=[],this.sortedValuesByBitCode=[],this.sortedBitCodes=[],this.sortedBitLengthsByBitCode=[],this.bitCodeToValue=[],!["byte","int"].includes(this.dataType))throw new TypeError(`${this.dataType} decoding not yet implemented by HUFFMAN_INT codec`);this.buildCodeBook(),this.buildCodes(),this.buildCaches(),0===this.sortedCodes[0].bitLength&&(this._decode=this._decodeZeroLengthCode)}buildCodeBook(){let t=new Array(this.parameters.numCodes);for(let e=0;et.bitLength-e.bitLength||t.symbol-e.symbol)),this.codeBook={},t.forEach((t=>{this.codeBook[t.bitLength]||(this.codeBook[t.bitLength]=[]),this.codeBook[t.bitLength].push(t.symbol)}))}buildCodes(){this.codes={};let t=0,e=-1;Object.entries(this.codeBook).forEach((([i,n])=>{const s=parseInt(i,10);n.forEach((i=>{const n={bitLength:s,value:i,bitCode:0};e+=1;const o=s-t;if(e<<=o,n.bitCode=e,t+=o,function(t){let e=t-(t>>1)&1431655765;return 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i=t;this.sortedCodes[i+1].bitLength===e&&i{Object.defineProperty(e,"__esModule",{value:!0}),e.default={CRAM_FLAG_PRESERVE_QUAL_SCORES:1,CRAM_FLAG_DETACHED:2,CRAM_FLAG_MATE_DOWNSTREAM:4,CRAM_FLAG_NO_SEQ:8,CRAM_FLAG_MASK:15,CRAM_M_REVERSE:1,CRAM_M_UNMAP:2,BAM_FPAIRED:1,BAM_FPROPER_PAIR:2,BAM_FUNMAP:4,BAM_FMUNMAP:8,BAM_FREVERSE:16,BAM_FMREVERSE:32,BAM_FREAD1:64,BAM_FREAD2:128,BAM_FSECONDARY:256,BAM_FQCFAIL:512,BAM_FDUP:1024,BAM_FSUPPLEMENTARY:2048,BAM_CMATCH:0,BAM_CINS:1,BAM_CDEL:2,BAM_CREF_SKIP:3,BAM_CSOFT_CLIP:4,BAM_CHARD_CLIP:5,BAM_CPAD:6,BAM_CEQUAL:7,BAM_CDIFF:8,BAM_CBACK:9,BAM_CIGAR_STR:"MIDNSHP:XB",BAM_CIGAR_SHIFT:4,BAM_CIGAR_MASK:15,BAM_CIGAR_TYPE:246183}},8543:(t,e,i)=>{Object.defineProperty(e,"__esModule",{value:!0});const n=i(8772),r=i(8577),s={BF:"int",CF:"int",RI:"int",RL:"int",AP:"int",RG:"int",MF:"int",NS:"int",NP:"int",TS:"int",NF:"int",TC:"byte",TN:"int",FN:"int",FC:"byte",FP:"int",BS:"byte",IN:"byteArray",SC:"byteArray",DL:"int",BA:"byte",BB:"byteArray",RS:"int",PD:"int",HC:"int",MQ:"int",RN:"byteArray",QS:"byte",QQ:"byteArray",TL:"int"};e.default=class{constructor(t){this.dataSeriesCodecCache={},this.tagCodecCache={},this.tagEncoding={},this.readNamesIncluded=t.preservation.RN,this.APdelta=t.preservation.AP,this.referenceRequired=!!t.preservation.RR,this.tagIdsDictionary=t.preservation.TD,this.substitutionMatrix=function(t){const e=new Array(5);for(let t=0;t<5;t+=1)e[t]=new Array(4);return e[0][t[0]>>6&3]="C",e[0][t[0]>>4&3]="G",e[0][t[0]>>2&3]="T",e[0][t[0]>>0&3]="N",e[1][t[1]>>6&3]="A",e[1][t[1]>>4&3]="G",e[1][t[1]>>2&3]="T",e[1][t[1]>>0&3]="N",e[2][t[2]>>6&3]="A",e[2][t[2]>>4&3]="C",e[2][t[2]>>2&3]="T",e[2][t[2]>>0&3]="N",e[3][t[3]>>6&3]="A",e[3][t[3]>>4&3]="C",e[3][t[3]>>2&3]="G",e[3][t[3]>>0&3]="N",e[4][t[4]>>6&3]="A",e[4][t[4]>>4&3]="C",e[4][t[4]>>2&3]="G",e[4][t[4]>>0&3]="T",e}(t.preservation.SM),this.dataSeriesEncoding=t.dataSeriesEncoding,this.tagEncoding=t.tagEncoding,this.preservation=t.preservation,this._size=t._size,this._endPosition=t._endPosition}getCodecForTag(t){if(!this.tagCodecCache[t]){const e=this.tagEncoding[t];e&&(this.tagCodecCache[t]=(0,n.instantiateCodec)(e,"byteArray"))}return this.tagCodecCache[t]}getTagNames(t){return this.tagIdsDictionary[t]}getCodecForDataSeries(t){let e=this.dataSeriesCodecCache[t];if(void 0===e){const i=this.dataSeriesEncoding[t];if(i){const o=s[t];if(!o)throw new r.CramMalformedError(`data series name ${t} not defined in 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t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const s=i(597),o=r(i(2779)),a=r(i(1269)),l=i(8577),h=r(i(9675)),c=i(6141),u=r(i(3498)),d=r(i(6284)),f=i(3427),p=i(9488),g=i(7578);class m{constructor(t){var e;if(this.file=(0,f.open)(t.url,t.path,t.filehandle),this.validateChecksums=!0,this.fetchReferenceSequenceCallback=t.seqFetch,this.options={checkSequenceMD5:t.checkSequenceMD5,cacheSize:null!==(e=t.cacheSize)&&void 0!==e?e:2e4},this.featureCache=new a.default({maxSize:this.options.cacheSize}),function(){const t=new Uint32Array([287454020]),e=new Uint8Array(t.buffer);return 68===e[0]?0:17===e[0]?1:2}()>0)throw new Error("Detected big-endian machine, may be unable to run")}read(t,e,i,n){return this.file.read(t,e,i,n)}stat(){return this.file.stat()}getDefinition(){return n(this,void 0,void 0,(function*(){const t=Buffer.allocUnsafe(c.cramFileDefinition.maxLength);yield this.file.read(t,0,c.cramFileDefinition.maxLength,0);const e=c.cramFileDefinition.parser.parse(t).result;if(2!==e.majorVersion&&3!==e.majorVersion)throw new l.CramUnimplementedError(`CRAM version ${e.majorVersion} not supported`);return e}))}getSamHeader(){return n(this,void 0,void 0,(function*(){const t=yield this.getContainerById(0);if(!t)throw new l.CramMalformedError("file contains no containers");const e=yield t.getFirstBlock();if(void 0===e)return(0,g.parseHeaderText)("");const i=e.content,n=i.readInt32LE(0),r=i.toString("utf8",4,4+n);return this.header=r,(0,g.parseHeaderText)(r)}))}getHeaderText(){return n(this,void 0,void 0,(function*(){return yield this.getSamHeader(),this.header}))}getSectionParsers(){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition();return(0,c.getSectionParsers)(t)}))}getContainerById(t){return n(this,void 0,void 0,(function*(){const e=yield this.getSectionParsers();let i=e.cramFileDefinition.maxLength;const{size:n}=yield this.file.stat(),{cramContainerHeader1:r}=e;let s;for(let e=0;e<=t;e+=1){if(i+r.maxLength+8>=n)return;s=this.getContainerAtPosition(i);const o=yield s.getHeader();if(!o)throw new l.CramMalformedError(`container ${t} not found in file`);if(0===e){i=o._endPosition;for(let t=0;t=n)return;const r=Buffer.allocUnsafe(i.maxLength);return yield this.file.read(r,0,i.maxLength,t),(0,p.parseItem)(r,i.parser,0,t)}))}_parseSection(t,e,i=t.maxLength,r){return n(this,void 0,void 0,(function*(){let n;if(r)n=r;else{const{size:t}=yield this.file.stat();if(e+i>=t)return;n=Buffer.allocUnsafe(i),yield this.file.read(n,0,i,e)}const s=(0,p.parseItem)(n,t.parser,0,e);if(s._size!==i)throw new l.CramMalformedError(`section read error: requested size ${i} does not equal parsed size ${s._size}`);return s}))}_uncompress(t,e,i){if("gzip"===t)(0,s.unzip)(e).copy(i);else if("bzip2"===t){const t=bzip2.array(e);let n,r=bzip2.header(t),s=0;do{n=bzip2.decompress(t,r),-1!=n&&(Buffer.from(n).copy(i,s),s+=n.length,r-=n.length)}while(-1!=n)}else if("rans"===t)(0,h.default)(e,i);else if("rans4x16"===t)u.default.r4x16_uncompress(e,i);else if("arith"===t)u.default.arith_uncompress(e,i);else if("fqzcomp"===t)u.default.fqzcomp_uncompress(e,i);else{if("tok3"!==t)throw new l.CramUnimplementedError(`${t} decompression not yet implemented`);u.default.tok3_uncompress(e,i)}}readBlock(t){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.getDefinition(),i=yield this.getSectionParsers(),n=yield this.readBlockHeader(t);if(void 0===n)return;const r=n._endPosition,s=Buffer.allocUnsafe(n.uncompressedSize),o=Object.assign(Object.assign({},n),{_endPosition:r,contentPosition:r,content:s});if("raw"!==n.compressionMethod){const t=Buffer.allocUnsafe(n.compressedSize);yield this.read(t,0,n.compressedSize,r),this._uncompress(n.compressionMethod,t,s)}else yield this.read(s,0,n.uncompressedSize,r);if(e>=3){const e=yield this._parseSection(i.cramBlockCrc32,r+n.compressedSize);if(void 0===e)return;o.crc32=e.crc32,this.validateChecksums&&(yield this.checkCrc32(t,n._size+n.compressedSize,e.crc32,"block data")),o._endPosition=e._endPosition,o._size=o.compressedSize+i.cramBlockCrc32.maxLength}else o._endPosition=r+o.compressedSize,o._size=o.compressedSize;return o}))}}e.default=m,"getDefinition getSectionParsers getSamHeader".split(" ").forEach((t=>(0,p.tinyMemoize)(m,t)))},8222:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0}),e.CramRecord=void 0;const r=n(i(5457));var s=i(8631);Object.defineProperty(e,"CramRecord",{enumerable:!0,get:function(){return n(s).default}}),e.default=r.default},8631:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0}),e.MateFlagsDecoder=e.CramFlagsDecoder=e.BamFlagsDecoder=e.MateFlags=e.CramFlags=e.BamFlags=void 0;const r=n(i(2615)),s={a:0,A:0,c:1,C:1,g:2,G:2,t:3,T:3,n:4,N:4};function o(t){const e={};for(const[i,n]of t)e["is"+n]=t=>!!(t&i),e["set"+n]=t=>t|i;return e}e.BamFlags=[[1,"Paired"],[2,"ProperlyPaired"],[4,"SegmentUnmapped"],[8,"MateUnmapped"],[16,"ReverseComplemented"],[32,"MateReverseComplemented"],[64,"Read1"],[128,"Read2"],[256,"Secondary"],[512,"FailedQc"],[1024,"Duplicate"],[2048,"Supplementary"]],e.CramFlags=[[1,"PreservingQualityScores"],[2,"Detached"],[4,"WithMateDownstream"],[8,"DecodeSequenceAsStar"]],e.MateFlags=[[1,"OnNegativeStrand"],[2,"Unmapped"]],e.BamFlagsDecoder=o(e.BamFlags),e.CramFlagsDecoder=o(e.CramFlags),e.MateFlagsDecoder=o(e.MateFlags),e.default=class{constructor({flags:t,cramFlags:e,readLength:i,mappingQuality:n,lengthOnRef:r,qualityScores:s,mateRecordNumber:o,readBases:a,readFeatures:l,mateToUse:h,readGroupId:c,readName:u,sequenceId:d,uniqueId:f,templateSize:p,alignmentStart:g,tags:m}){this.flags=t,this.cramFlags=e,this.readLength=i,this.mappingQuality=n,this.lengthOnRef=r,this.qualityScores=s,a&&(this.readBases=a),this.readGroupId=c,this.readName=u,this.sequenceId=d,this.uniqueId=f,this.templateSize=p,this.alignmentStart=g,this.tags=m,l&&(this.readFeatures=l),h&&(this.mate={flags:h.mateFlags,readName:h.mateReadName,sequenceId:h.mateSequenceId,alignmentStart:h.mateAlignmentStart}),o&&(this.mateRecordNumber=o)}isPaired(){return!!(this.flags&r.default.BAM_FPAIRED)}isProperlyPaired(){return!!(this.flags&r.default.BAM_FPROPER_PAIR)}isSegmentUnmapped(){return!!(this.flags&r.default.BAM_FUNMAP)}isMateUnmapped(){return!!(this.flags&r.default.BAM_FMUNMAP)}isReverseComplemented(){return!!(this.flags&r.default.BAM_FREVERSE)}isMateReverseComplemented(){return!!(this.flags&r.default.BAM_FMREVERSE)}isRead1(){return!!(this.flags&r.default.BAM_FREAD1)}isRead2(){return!!(this.flags&r.default.BAM_FREAD2)}isSecondary(){return!!(this.flags&r.default.BAM_FSECONDARY)}isFailedQc(){return!!(this.flags&r.default.BAM_FQCFAIL)}isDuplicate(){return!!(this.flags&r.default.BAM_FDUP)}isSupplementary(){return!!(this.flags&r.default.BAM_FSUPPLEMENTARY)}isDetached(){return!!(this.cramFlags&r.default.CRAM_FLAG_DETACHED)}hasMateDownStream(){return!!(this.cramFlags&r.default.CRAM_FLAG_MATE_DOWNSTREAM)}isPreservingQualityScores(){return!!(this.cramFlags&r.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)}isUnknownBases(){return!!(this.cramFlags&r.default.CRAM_FLAG_NO_SEQ)}getReadBases(){if(!this.readBases&&this._refRegion){const t=function(t,e){if(!t.lengthOnRef&&!t.readLength)return null;if(t.isUnknownBases())return null;const i=t.alignmentStart-e.start;if(!t.readFeatures)return e.seq.substr(i,t.lengthOnRef).toUpperCase();let n="",r=i,s=0;for(;n.lengththis.mate.alignmentStart&&s>0&&(s=-s),s>0?(r[0]=t,r[1]=i,r[2]=e,r[3]=n):(r[2]=t,r[3]=i,r[0]=e,r[1]=n),r.join("")}return null}addReferenceSequence(t,e){this.readFeatures&&this.readFeatures.forEach((i=>{"X"===i.code&&function(t,e,i,n){if(!e)return;const r=n.refPos-e.start,o=e.seq.charAt(r);o&&(n.ref=o);let a=s[o];void 0===a&&(a=4);const l=i.substitutionMatrix[a][n.data];l&&(n.sub=l)}(0,t,e,i)})),!this.readBases&&t.start<=this.alignmentStart&&t.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=t)}toJSON(){const t={};return Object.keys(this).forEach((e=>{"_"!==e.charAt(0)&&(t[e]=this[e])})),t.readBases=this.getReadBases(),t}}},6141:(t,e,i)=>{Object.defineProperty(e,"__esModule",{value:!0}),e.getSectionParsers=e.cramFileDefinition=e.isMappedSliceHeader=void 0;const n=i(9996),r=(new n.Parser).itf8(),s={parser:(new n.Parser).string("magic",{length:4}).uint8("majorVersion").uint8("minorVersion").string("fileId",{length:20,stripNull:!0}),maxLength:26};e.cramFileDefinition=s;const o={parser:(new n.Parser).uint8("compressionMethod",{formatter:t=>{const e=["raw","gzip","bzip2","lzma","rans","rans4x16","arith","fqzcomp","tok3"][t];if(!e)throw new Error(`compression method number ${t} not implemented`);return e}}).uint8("contentType",{formatter:t=>{const e=["FILE_HEADER","COMPRESSION_HEADER","MAPPED_SLICE_HEADER","UNMAPPED_SLICE_HEADER","EXTERNAL_DATA","CORE_DATA"][t];if(!e)throw new Error(`invalid block content type id ${t}`);return e}}).itf8("contentId").itf8("compressedSize").itf8("uncompressedSize"),maxLength:17},a={parser:(new n.Parser).uint32("crc32"),maxLength:4},l=(new n.Parser).itf8("size").buffer("ents",{length:"size",formatter:t=>{function e(e,i){const n=t.toString("utf8",e,i),r=[];for(let t=0;tr&&n.push(e(r,i)),n}}),h=(new n.Parser).uint8(null,{formatter:t=>!!t}),c=(new n.Parser).itf8("mapSize").itf8("mapCount").array("ents",{length:"mapCount",type:(new n.Parser).string("key",{length:2,stripNull:!1}).choice("value",{tag:"key",choices:{MI:h,UI:h,PI:h,RN:h,AP:h,RR:h,SM:(new n.Parser).array(null,{type:"uint8",length:5}),TD:(new n.Parser).nest(null,{type:l,formatter:t=>t.ents})}})});function u(t){const e={};for(let i=0;i=3?(i=i.ltf8("recordCounter"),e+=9):2===t&&(i=i.itf8("recordCounter"),e+=5),i=i.itf8("numBlocks").itf8("numContentIds").array("contentIds",{type:r,length:"numContentIds"}),e+=10,t>=2&&(i=i.array("md5",{type:"uint8",length:16}),e+=16),{parser:i,maxLength:t=>e+5*t}},cramMappedSliceHeader(t){let e=(new n.Parser).itf8("refSeqId").itf8("refSeqStart").itf8("refSeqSpan").itf8("numRecords"),i=20;return t>=3?(e=e.ltf8("recordCounter"),i+=9):2===t&&(e=e.itf8("recordCounter"),i+=5),e=e.itf8("numBlocks").itf8("numContentIds").array("contentIds",{type:r,length:"numContentIds"}).itf8("refBaseBlockId"),i+=15,t>=2&&(e=e.array("md5",{type:"uint8",length:16}),i+=16),{parser:e,maxLength:t=>i+5*t}},cramEncoding:t=>({parser:(new n.Parser).namely("cramEncoding").itf8("codecId").itf8("parametersBytes").choice("parameters",{tag:"codecId",choices:{0:new n.Parser,1:(new n.Parser).itf8("blockContentId"),2:(new n.Parser).itf8("offset").itf8("M"),3:n.Parser.start().itf8("numCodes").array("symbols",{length:"numCodes",type:r}).itf8("numLengths").array("bitLengths",{length:"numLengths",type:r}),4:n.Parser.start().nest("lengthsEncoding",{type:"cramEncoding"}).nest("valuesEncoding",{type:"cramEncoding"}),5:(new n.Parser).uint8("stopByte").itf8("blockContentId"),6:(new n.Parser).itf8("offset").itf8("length"),7:(new n.Parser).itf8("offset").itf8("K"),8:(new n.Parser).itf8("offset").itf8("log2m"),9:(new n.Parser).itf8("offset")}})}),cramDataSeriesEncodingMap(t){return(new n.Parser).itf8("mapSize").itf8("mapCount").array("ents",{length:"mapCount",type:(new n.Parser).string("key",{length:2,stripNull:!1}).nest("value",{type:this.cramEncoding(t).parser})})},cramTagEncodingMap(t){return(new n.Parser).itf8("mapSize").itf8("mapCount").array("ents",{length:"mapCount",type:(new n.Parser).itf8("key",{formatter:t=>String.fromCharCode(t>>16&255)+String.fromCharCode(t>>8&255)+String.fromCharCode(255&t)}).nest("value",{type:this.cramEncoding(t).parser})})},cramCompressionHeader(t){let e=new n.Parser;return e=e.nest("preservation",{type:c,formatter:u}).nest("dataSeriesEncoding",{type:this.cramDataSeriesEncodingMap(t),formatter:u}).nest("tagEncoding",{type:this.cramTagEncodingMap(t),formatter:u}),{parser:e}},cramContainerHeader1(t){let e=(new n.Parser).int32("length").itf8("refSeqId").itf8("refSeqStart").itf8("alignmentSpan").itf8("numRecords"),i=24;return t>=3?(e=e.ltf8("recordCounter"),i+=9):2===t&&(e=e.itf8("recordCounter"),i+=5),t>1&&(e=e.ltf8("numBases"),i+=9),e=e.itf8("numBlocks").itf8("numLandmarks"),i+=10,{parser:e,maxLength:i}},cramContainerHeader2(t){let e=(new n.Parser).itf8("numLandmarks").array("landmarks",{type:(new n.Parser).itf8(),length:"numLandmarks"}),i=0;return t>=3&&(e=e.uint32("crc32"),i=4),{parser:e,maxLength:t=>5+5*t+i}}};e.getSectionParsers=function(t){const e=Object.assign({},d);return Object.keys(f).forEach((i=>{e[i]=f[i](t)})),e}},3757:function(t,e,i){var n=this&&this.__importDefault||function(t){return t&&t.__esModule?t:{default:t}};Object.defineProperty(e,"__esModule",{value:!0});const r=n(i(3720)),s=i(8577),o=i(8631),a=i(6141);function l(t){let e="";for(let i=0;i1&&-2===n.parsedContent.refSeqId?e("RI"):n.parsedContent.refSeqId;const b=e("RL");let y=e("AP");i.APdelta&&(y+=u.lastAlignmentStart),u.lastAlignmentStart=y;const v=e("RG");let w,_,x,k;if(i.readNamesIncluded&&(w=l(e("RN"))),o.CramFlagsDecoder.isDetached(g)){const t=e("MF");let n;i.readNamesIncluded||(n=l(e("RN")),w=n);const r=e("NS"),s=e("NP");(t||r>-1)&&(_={mateFlags:t,mateSequenceId:r,mateAlignmentStart:s,mateReadName:n}),x=e("TS"),o.MateFlagsDecoder.isUnmapped(t)&&(p=o.BamFlagsDecoder.setMateUnmapped(p)),o.MateFlagsDecoder.isOnNegativeStrand(t)&&(p=o.BamFlagsDecoder.setMateReverseComplemented(p))}else o.CramFlagsDecoder.isWithMateDownstream(g)&&(k=e("NF")+f+1);const S=e("TL");if(S<0)throw new s.CramMalformedError("invalid TL index");const C={},A=i.getTagNames(S),T=A.length;for(let e=0;e1?"SC":"IN"],X:["number","BS"],D:["number","DL"],I:["string","IN"],i:["character","BA"],b:["string","BB"],q:["numArray","QQ"],Q:["number","QS"],H:["number","HC"],P:["number","PD"],N:["number","RS"]}[e];if(!c)throw new s.CramMalformedError(`invalid read feature code "${e}"`);let u=h(c);const d={B:["number","QS"]}[e];d&&(u=[u,h(d)]),o+=n;const f=o;a+=n;const p=a;"D"===e||"N"===e?a+=u:"I"===e||"S"===e?a-=u.length:"i"===e&&(a-=1),l[t]={code:e,pos:f,refPos:p,data:u}}return l}(y,t,e,0,d)),E=b,I)for(const{code:t,data:e}of I)"D"===t||"N"===t?E+=e:"I"===t||"S"===t?E-=e.length:"i"===t&&(E-=1);if(Number.isNaN(E)&&(console.warn(`${w||`${m}:${y}`} record has invalid read features`),E=b),M=e("MQ"),o.CramFlagsDecoder.isPreservingQualityScores(g)){R=new Array(b);for(let t=0;t=0){const r=t[i.mateRecordNumber];if(!r)throw new s.CramMalformedError("intra-slice mate record not found, this file seems malformed");n.push(...e(r))}return n}(i),r=n.map((t=>t.alignmentStart)),o=n.map((t=>t.alignmentStart+t.readLength-1)),a=Math.max(...o)-Math.min(...r)+1;a>=0&&n.forEach((t=>{if(void 0!==t.templateLength)throw new s.CramMalformedError("mate pair group has some members that have template lengths already, this file seems malformed");t.templateLength=a}))}(t,0,i):function(t,e){const i=Math.min(t.alignmentStart,e.alignmentStart),n=Math.max(t.alignmentStart+t.readLength-1,e.alignmentStart+e.readLength-1)-i+1;t.templateLength=n,e.templateLength=n}(i,n)),delete i.mateRecordNumber}class f{constructor(t,e,i){this.container=t,this.containerPosition=e,this.file=t.file}getHeader(){return n(this,void 0,void 0,(function*(){const t=yield this.file.getSectionParsers(),e=yield this.container.getHeader(),i=yield this.file.readBlock(e._endPosition+this.containerPosition);if(void 0===i)throw new Error;if("MAPPED_SLICE_HEADER"===i.contentType){const n=(0,o.parseItem)(i.content,t.cramMappedSliceHeader.parser,0,e._endPosition);return Object.assign(Object.assign({},i),{parsedContent:n})}if("UNMAPPED_SLICE_HEADER"===i.contentType){const n=(0,o.parseItem)(i.content,t.cramUnmappedSliceHeader.parser,0,e._endPosition);return Object.assign(Object.assign({},i),{parsedContent:n})}throw new s.CramMalformedError(`error reading slice header block, invalid content type ${i.contentType}`)}))}getBlocks(){return n(this,void 0,void 0,(function*(){const t=yield this.getHeader();let e=t._endPosition;const i=new Array(t.parsedContent.numBlocks);for(let t=0;t{"EXTERNAL_DATA"===t.contentType&&(e[t.contentId]=t)})),e}))}getBlockByContentId(t){return n(this,void 0,void 0,(function*(){return(yield this._getBlocksContentIdIndex())[t]}))}getReferenceRegion(){return n(this,void 0,void 0,(function*(){const t=(yield this.getHeader()).parsedContent;if(!(0,c.isMappedSliceHeader)(t))throw new Error;if(t.refSeqId<0)return;const e=yield this.container.getCompressionScheme();if(void 0===e)throw new Error;if(t.refBaseBlockId>=0){const e=yield this.getBlockByContentId(t.refBaseBlockId);if(!e)throw new s.CramMalformedError("embedded reference specified, but reference block does not exist");return{seq:e.data.toString("utf8"),start:t.refSeqStart,end:t.refSeqStart+t.refSeqSpan-1,span:t.refSeqSpan}}if(e.referenceRequired||this.file.fetchReferenceSequenceCallback){if(!this.file.fetchReferenceSequenceCallback)throw new Error("reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence");const e=yield this.file.fetchReferenceSequenceCallback(t.refSeqId,t.refSeqStart,t.refSeqStart+t.refSeqSpan-1);if(e.length!==t.refSeqSpan)throw new s.CramArgumentError("seqFetch callback returned a reference sequence of the wrong length");return{seq:e,start:t.refSeqStart,end:t.refSeqStart+t.refSeqSpan-1,span:t.refSeqSpan}}}))}getAllRecords(){return this.getRecords((()=>!0))}_fetchRecords(){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.file.getDefinition(),e=yield this.container.getCompressionScheme();if(void 0===e)throw new Error;const i=yield this.getHeader();if(void 0===i)throw new Error;const n=yield this._getBlocksContentIdIndex();if(t>1&&this.file.options.checkSequenceMD5&&(0,c.isMappedSliceHeader)(i.parsedContent)&&i.parsedContent.refSeqId>=0&&"0000000000000000"!==i.parsedContent.md5.join("")){const t=yield this.getReferenceRegion();if(t){const{seq:e,start:n,end:r}=t,a=(0,o.sequenceMD5)(e),l=i.parsedContent.md5.map((t=>(t<16?"0":"")+t.toString(16))).join("");if(a!==l)throw new s.CramMalformedError(`MD5 checksum reference mismatch for ref ${i.parsedContent.refSeqId} pos ${n}..${r}. recorded MD5: ${l}, calculated MD5: ${a}`)}}const r=yield this.getCoreDataBlock(),a={lastAlignmentStart:(0,c.isMappedSliceHeader)(i.parsedContent)?i.parsedContent.refSeqStart:0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{map:new Map,getCursor(t){let e=this.map.get(t);return void 0===e&&(e={bitPosition:7,bytePosition:0},this.map.set(t,e)),e}}},f=t=>{const i=e.getCodecForDataSeries(t);if(!i)throw new s.CramMalformedError(`no codec defined for ${t} data series`);return i.decode(this,r,n,a)};let p=new Array(i.parsedContent.numRecords);for(let s=0;s!!t));break}throw t}for(let t=0;t=0&&d(p,t,p[t],p[e])}return p}))}getRecords(t){return n(this,void 0,void 0,(function*(){const 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this.next&&(t=this.next.generate(t)),t},Object.keys(l).forEach((function(t){f.prototype["generate".concat(t)]=function(e){"UInt64"===t?e.pushCode("{0} = Long.fromBytes(buffer.slice(offset,offset+8), true, this.endian === 'le').toNumber();",e.generateVariable(this.varName),t):"Int64"===t?e.pushCode("{0} = Long.fromBytes(buffer.slice(offset,offset+8), false, this.endian === 'le').toNumber();",e.generateVariable(this.varName),t):e.pushCode("{0} = buffer.read{1}(offset);",e.generateVariable(this.varName),t),e.pushCode("offset += {0};",l[t])}})),f.prototype.generateBit=function(t){var e=JSON.parse(JSON.stringify(this));if(e.varName=t.generateVariable(e.varName),t.bitFields.push(e),!this.next||this.next&&["Bit","Nest"].indexOf(this.next.type)<0){var i=0;t.bitFields.forEach((function(t){i+=t.options.length}));var n=t.generateTmpVariable();if(i<=8)t.pushCode("var {0} = buffer.readUInt8(offset);",n),i=8;else if(i<=16)t.pushCode("var {0} = buffer.readUInt16BE(offset);",n),i=16;else if(i<=24){var r=t.generateTmpVariable(),s=t.generateTmpVariable();t.pushCode("var {0} = buffer.readUInt16BE(offset);",r),t.pushCode("var {0} = buffer.readUInt8(offset + 2);",s),t.pushCode("var {2} = ({0} << 8) | {1};",r,s,n),i=24}else{if(!(i<=32))throw new Error("Currently, bit field sequence longer than 4-bytes is not supported.");t.pushCode("var {0} = buffer.readUInt32BE(offset);",n),i=32}t.pushCode("offset += {0};",i/8);var o=0,a="be"===this.endian;t.bitFields.forEach((function(e){t.pushCode("{0} = {1} >> {2} & {3};",e.varName,n,a?i-o-e.options.length:o,(1< offset++);"),t.pushCode("{0} = buffer.toString('{1}', {2}, offset);",e,this.options.encoding,i)),this.options.stripNull&&t.pushCode("{0} = {0}.replace(/\\x00+$/g, '')",e)},f.prototype.generateBuffer=function(t){"eof"===this.options.readUntil?t.pushCode("{0} = buffer.slice(offset);",t.generateVariable(this.varName)):(t.pushCode("{0} = buffer.slice(offset, offset + {1});",t.generateVariable(this.varName),t.generateOption(this.options.length)),t.pushCode("offset += {0};",t.generateOption(this.options.length))),this.options.clone&&t.pushCode("{0} = Buffer.from({0});",t.generateVariable(this.varName))},f.prototype.generateArray=function(t){var e=t.generateOption(this.options.length),i=t.generateOption(this.options.lengthInBytes),n=this.options.type,r=t.generateTmpVariable(),s=t.generateVariable(this.varName),o=t.generateTmpVariable(),a=this.options.key,u="string"==typeof a;if(u?t.pushCode("{0} = {};",s):t.pushCode("{0} = [];",s),"function"==typeof this.options.readUntil?t.pushCode("do {"):"eof"===this.options.readUntil?t.pushCode("for (var {0} = 0; offset < buffer.length; {0}++) {",r):void 0!==i?t.pushCode("for (var {0} = offset; offset - {0} < {1}; ) {",r,i):t.pushCode("for (var {0} = 0; {0} < {1}; {0}++) {",r,e),"string"==typeof n)if(h[n]){var p=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",p,c+n),t.pushCode("var {0} = {1}.result; offset = {1}.offset;",o,p),n!==this.alias&&t.addReference(n)}else t.pushCode("var {0} = buffer.read{1}(offset);",o,d[n]),t.pushCode("offset += {0};",l[d[n]]);else n instanceof f&&(t.pushCode("var {0} = {};",o),t.pushScope(o),n.generate(t),t.popScope());u?t.pushCode("{0}[{2}.{1}] = {2};",s,a,o):t.pushCode("{0}.push({1});",s,o),t.pushCode("}"),"function"==typeof this.options.readUntil&&t.pushCode(" while (!({0}).call(this, {1}, buffer.slice(offset)));",this.options.readUntil,o)},f.prototype.generateChoiceCase=function(t,e,i){if("string"==typeof i)if(h[i]){var n=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",n,c+i),t.pushCode("{0} = {1}.result; offset = {1}.offset;",t.generateVariable(this.varName),n),i!==this.alias&&t.addReference(i)}else t.pushCode("{0} = buffer.read{1}(offset);",t.generateVariable(this.varName),d[i]),t.pushCode("offset += {0};",l[d[i]]);else i instanceof f&&(t.pushPath(e),i.generate(t),t.popPath(e))},f.prototype.generateChoice=function(t){var e=t.generateOption(this.options.tag);this.varName&&t.pushCode("{0} = {};",t.generateVariable(this.varName)),t.pushCode("switch({0}) {",e),Object.keys(this.options.choices).forEach((function(e){var i=this.options.choices[e];Number.isNaN(parseInt(e,10))?t.pushCode("case '{0}':",e):t.pushCode("case {0}:",e),this.generateChoiceCase(t,this.varName,i),t.pushCode("break;")}),this),t.pushCode("default:"),this.options.defaultChoice?this.generateChoiceCase(t,this.varName,this.options.defaultChoice):t.generateError('"Met undefined tag value " + {0} + " at choice"',e),t.pushCode("}")},f.prototype.generateNest=function(t){var e=t.generateVariable(this.varName);if(this.options.type instanceof f)this.varName&&t.pushCode("{0} = {};",e),t.pushPath(this.varName),this.options.type.generate(t),t.popPath(this.varName);else if(h[this.options.type]){var i=t.generateTmpVariable();t.pushCode("var {0} = {1}(offset);",i,c+this.options.type),t.pushCode("{0} = {1}.result; offset = {1}.offset;",e,i),this.options.type!==this.alias&&t.addReference(this.options.type)}},f.prototype.generateFormatter=function(t,e,i){"function"==typeof i&&t.pushCode("{0} = ({1}).call(this, {0});",e,i)},f.prototype.isInteger=function(){return!!this.type.match(/U?Int[8|16|32][BE|LE]?|Bit\d+/)},f.prototype.itf8=function(t,e){return this.setNextParser("itf8",t,e)},f.prototype.itf8=function(t,e){return this.setNextParser("itf8",t,e)},f.prototype.generateItf8=function(t){var e=t.generateVariable(this.varName),i=t.generateTmpVariable();t.pushCode("\n var ".concat(i," = buffer[offset];\n if (").concat(i," < 0x80) {\n ").concat(e," = ").concat(i,";\n offset += 1;\n } else if (").concat(i," < 0xc0) {\n ").concat(e," = ((").concat(i,"<<8) | buffer[offset+1]) & 0x3fff;\n offset += 2;\n } else if (").concat(i," < 0xe0) {\n ").concat(e," = ((").concat(i,"<<16) | (buffer[offset+1]<< 8) | buffer[offset+2]) & 0x1fffff;\n offset += 3;\n } else if (").concat(i," < 0xf0) {\n ").concat(e," = ((").concat(i,"<<24) | (buffer[offset+1]<<16) | (buffer[offset+2]<<8) | buffer[offset+3]) & 0x0fffffff;\n offset += 4\n } else {\n ").concat(e," = ((").concat(i," & 0x0f)<<28) | (buffer[offset+1]<<20) | (buffer[offset+2]<<12) | (buffer[offset+3]<<4) | (buffer[offset+4] & 0x0f);\n // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);\n // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;\n offset += 5\n }\n "))},f.prototype.ltf8=function(t,e){return this.setNextParser("ltf8",t,e)},f.prototype.generateLtf8=function(t){var e=t.generateVariable(this.varName),i=t.generateTmpVariable();t.pushCode("\n var ".concat(i," = buffer[offset];\n if (").concat(i," < 0x80) {\n ").concat(e," = ").concat(i,";\n offset += 1;\n } else if (").concat(i," < 0xc0) {\n ").concat(e," = ((buffer[offset]<<8) | buffer[offset+1]) & 0x3fff;\n offset += 2;\n } else if (").concat(i," < 0xe0) {\n ").concat(e," = ((buffer[offset]<<16) | (buffer[offset+1]<<8) | buffer[offset+2]) & 0x1fffff;\n ").concat(e," = (((").concat(i," & 63) << 16) | buffer.readUInt16LE(offset + 1));\n offset += 3;\n } else if (").concat(i," < 0xf0) {\n ").concat(e," = ((buffer[offset]<<24) | (buffer[offset+1]<<16) | (buffer[offset+2]<<8) | buffer[offset+3]) & 0x0fffffff;\n offset += 4;\n } else if (").concat(i," < 0xf8) {\n ").concat(e," = (((buffer[offset] & 15) * Math.pow(2,32))) +\n (buffer[offset+1]<<24) | (buffer[offset+2]<<16 | buffer[offset+3]<<8 | buffer[offset+4])\n // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;\n offset += 5;\n } else if (").concat(i," < 0xfc) {\n ").concat(e," = ((((buffer[offset] & 7) << 8) | buffer[offset+1] )) * Math.pow(2,32) +\n (buffer[offset+2]<<24) | (buffer[offset+3]<<16 | buffer[offset+4]<<8 | buffer[offset+5])\n offset += 6;\n } else if (").concat(i," < 0xfe) {\n ").concat(e," = ((((buffer[offset] & 3) << 16) | buffer[offset+1]<<8 | buffer[offset+2])) * Math.pow(2,32) +\n (buffer[offset+3]<<24) | (buffer[offset+4]<<16 | buffer[offset+5]<<8 | buffer[offset+6])\n offset += 7;\n } else if (").concat(i," < 0xff) {\n ").concat(e," = Long.fromBytesBE(buffer.slice(offset+1,offset+8));\n if (").concat(e,".greaterThan(Number.MAX_SAFE_INTEGER) || ").concat(e,".lessThan(Number.MIN_SAFE_INTEGER))\n throw new Error('integer overflow')\n ").concat(e," = ").concat(e,".toNumber()\n offset += 8;\n } else {\n ").concat(e," = Long.fromBytesBE(buffer.slice(offset+1,offset+9));\n if (").concat(e,".greaterThan(Number.MAX_SAFE_INTEGER) || ").concat(e,".lessThan(Number.MIN_SAFE_INTEGER))\n throw new Error('integer overflow')\n ").concat(e," = ").concat(e,".toNumber()\n offset += 9;\n }\n "))},e.Parser=f},2961:(t,e)=>{function i(t){return i="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t},i(t)}var n=function(){this.code="",this.scopes=[["vars"]],this.isAsync=!1,this.bitFields=[],this.tmpVariableCount=0,this.references={}};n.prototype.generateVariable=function(t){var e=[];for(Array.prototype.push.apply(e,this.scopes[this.scopes.length-1]);/^\$parent\./.test(t);)e.pop(),t=t.replace(/^\$parent\./,"");return t&&e.push(t),e.join(".")},n.prototype.generateOption=function(t){switch(i(t)){case"number":return t.toString();case"string":return this.generateVariable(t);case"function":return"(".concat(t,").call(").concat(this.generateVariable(),", vars)");default:return}},n.prototype.generateError=function(){var t=Array.prototype.slice.call(arguments),e=n.interpolate.apply(this,t);this.isAsync?this.pushCode("return process.nextTick(function() { callback(new Error(".concat(e,"), vars); });")):this.pushCode("throw new Error(".concat(e,");"))},n.prototype.generateTmpVariable=function(){return"$tmp".concat(this.tmpVariableCount++)},n.prototype.pushCode=function(){var t=Array.prototype.slice.call(arguments);this.code+="".concat(n.interpolate.apply(this,t),"\n")},n.prototype.pushPath=function(t){t&&this.scopes[this.scopes.length-1].push(t)},n.prototype.popPath=function(t){t&&this.scopes[this.scopes.length-1].pop()},n.prototype.pushScope=function(t){this.scopes.push([t])},n.prototype.popScope=function(){this.scopes.pop()},n.prototype.addReference=function(t){this.references[t]||(this.references[t]={resolved:!1,requested:!1})},n.prototype.markResolved=function(t){this.references[t].resolved=!0},n.prototype.markRequested=function(t){t.forEach(function(t){this.references[t].requested=!0}.bind(this))},n.prototype.getUnresolvedReferences=function(){var t=this.references;return Object.keys(this.references).filter((function(e){return!t[e].resolved&&!t[e].requested}))},n.interpolate=function(t){var e=t.match(/{\d+}/g),i=Array.prototype.slice.call(arguments,1);return e&&e.forEach((function(e){var n=parseInt(e.substr(1,e.length-2),10);t=t.replace(e,i[n].toString())})),t},e._=n},22:t=>{t.exports.runInThisContext=function(t){return new Function("code","return eval(code);").call(globalThis,t)}},445:(t,e,i)=>{const n=i(7381),r=i(9260),s=i(576),o=i(4693),a=128;t.exports=class{decode(t){return this.stream=new r(t),this.decodeStream(this.stream)}decodeStream(t,e=0){var i=this.stream.ReadByte();16&i||(e=this.stream.ReadUint7());var n,r=e,s=1&i;if(8&i)return this.decodeStripe(this.stream,e);if(i&a&&([n,r]=this.decodePackMeta(this.stream)),32&i)var o=this.decodeCat(this.stream,r);else o=4&i?this.decodeExt(this.stream,r):64&i?s?this.decodeRLE1(this.stream,r):this.decodeRLE0(this.stream,r):s?this.decode1(this.stream,r):this.decode0(this.stream,r);return i&a&&(o=this.decodePack(o,n,e)),o}encode(t,e){if(this.stream=new r("",0,1.1*t.length+100),this.stream.WriteByte(e),16&e||this.stream.WriteUint7(t.length),8&e)return Buffer.concat([this.stream.buf.slice(0,this.stream.pos),this.encodeStripe(this.stream,t,e>>8)]);var i,n=1&e,s=t.length;return e&a&&([i,t,s]=this.encodePack(t)),e&a&&this.stream.WriteStream(i),64&e?n?this.encodeRLE1(t,s,this.stream):this.encodeRLE0(t,s,this.stream):n?this.encode1(t,s,this.stream):this.encode0(t,s,this.stream)}decode0(t,e){var i=new Buffer.allocUnsafe(e),r=t.ReadByte();0==r&&(r=256);var o=new s(r),a=new n(t);a.RangeStartDecode(t);for(var l=0;l=3?3:c;for(l[u].ModelEncode(i,h,d),c-=d,u=256;3==d;)d=c>=3?3:c,l[u].ModelEncode(i,h,d),u=257,c-=d}return h.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeRLE1(t,e){var i=new Buffer.allocUnsafe(e),r=t.ReadByte();0==r&&(r=256);for(var o=new Array(r),a=0;a=3?3:u;for(l[d].ModelEncode(i,h,f),u-=f,d=256;3==f;)f=u>=3?3:u,l[d].ModelEncode(i,h,f),d=257,u-=f}return h.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodePackMeta(t){this.nsym=t.ReadByte();for(var e=new Array(this.nsym),i=0;i>=1}}else if(this.nsym<=4)for(r=0,s=0;r>=2;else{if(!(this.nsym<=16))return t;for(r=0,s=0;r>=4}return n}packMeta(t){for(var e=new r("",0,1024),i=new Array(256),n=0;no),n[o]=new Array(s[o]);for(var a=0,l=0;ls),o[s]=this.decodeStream(t,r[s]);var a=new Buffer.allocUnsafe(e);for(s=0;s{t.exports=class{constructor(t){this.low=0,this.range=4294967295,this.code=0,this.FFnum=0,this.carry=0,this.cache=0}RangeStartDecode(t){for(var e=0;e<5;e++)this.code=(this.code<<8)+t.ReadByte();this.code&=4294967295,this.code>>>=0}RangeGetFrequency(t){return this.range=Math.floor(this.range/t),Math.floor(this.code/this.range)}RangeDecode(t,e,i,n){for(this.code-=e*this.range,this.range*=i;this.range<1<<24;)this.range*=256,this.code=256*this.code+t.ReadByte()}RangeShiftLow(t){if(this.low<4278190080|this.carry){for(t.WriteByte(this.cache+this.carry);this.FFnum;)t.WriteByte(this.carry-1),this.FFnum--;this.cache=this.low>>>24,this.carry=0}else this.FFnum++;this.low<<=8,this.low>>>=0}RangeEncode(t,e,i,n){var r=this.low;for(this.range=Math.floor(this.range/n),this.low+=e*this.range,this.low>>>=0,this.range*=i,this.low{t.exports=class{constructor(t=256){this.total_freq=t,this.max_sym=t-1,this.S=new Array,this.F=new Array;for(var e=0;e<=this.max_sym;e++)this.S[e]=e,this.F[e]=1}ModelDecode(t,e){for(var i=e.RangeGetFrequency(this.total_freq),n=0,r=0;n+this.F[r]<=i;)n+=this.F[r++];e.RangeDecode(t,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise();var s=this.S[r];if(r>0&&this.F[r]>this.F[r-1]){var o=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=o,o=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=o}return s}ModelRenormalise(){this.total_freq=0;for(var t=0;t<=this.max_sym;t++)this.F[t]-=Math.floor(this.F[t]/2),this.total_freq+=this.F[t]}ModelEncode(t,e,i){for(var n=0,r=0;this.S[r]!=i;r++)n+=this.F[r];if(e.RangeEncode(t,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise(),i=this.S[r],r>0&&this.F[r]>this.F[r-1]){var s=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=s,s=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=s}}}},5260:(t,e,i)=>{const n=i(9260),r=i(576),s=i(7381);function o(t,e,i){for(var n=0,r=0,s=-1,o=new Array(1024);r>4,e.qshift=15&i,i=t.ReadByte(),e.qloc=i>>4,e.sloc=15&i,i=t.ReadByte(),e.ploc=i>>4,e.dloc=15&i,e.qmap=new Array(256),16&e.pflags)for(var n=0;n0&&128&e.pflags)o(t,e.qtab,256);else for(n=0;n<256;n++)e.qtab[n]=n;return e.ptab=new Array(1024),32&e.pflags&&o(t,e.ptab,1024),e.dtab=new Array(256),64&e.pflags&&o(t,e.dtab,256),e}function h(t,e,i,n,r,s){i.max_sel>0?r.s=n.sel.ModelDecode(t,e):r.s=0,r.x=i.stab[r.s];var o=i.params[r.x];if(o.fixed_len>=0){var a=n.len[0].ModelDecode(t,e);a|=n.len[1].ModelDecode(t,e)<<8,a|=n.len[2].ModelDecode(t,e)<<16,a|=n.len[3].ModelDecode(t,e)<<24,o.fixed_len>0&&(o.fixed_len=-a)}else a=-o.fixed_len;r.len=a,i.do_rev&&(s[r.rec]=n.rev.ModelDecode(t,e)),r.is_dup=0,2&o.pflags&&n.dup.ModelDecode(t,e)&&(r.is_dup=1),r.p=a,r.delta=0,r.qctx=0,r.prevq=0,r.rec++}function c(t,e,i){for(var n=0,r=0,s=new Array(2*i),o=0;n1?i.nparam-1:0,s=new Array(256);if(2&i)r=t.ReadByte(),o(t,s,256);else{for(var a=0;a0&&(e.sel=new r(t.max_sel+1)),e}(n),f=new s(t);f.RangeStartDecode(t);for(var p=new Buffer.allocUnsafe(i),g={qctx:0,prevq:0,delta:0,p:0,s:0,x:0,len:0,is_dup:0,rec:0},m=0;m0&&d.dup.ModelDecode(t,f)){for(var b=0;b4),qshift:u,qloc:7,pbits:7,pshift:e[0]>128?1:0,ploc:0,dbits:u>4?0:1,dshift:3,dloc:15,sbits:0,sloc:15,do_stab:0,context:0,max_sym:l,nsym:a,do_qmap:d,do_dedup:0,fixed_len:1==e.length?1:0,do_sel:0,do_rev:0,do_pos:1,do_delta:u<=4?1:0,do_qtab:0,qbits:8+(u>4)-(0==o),sbits:1,sloc:15-(u<=4),do_stab:1,do_sel:1}]}(t,e,i,o),p=function(t,e,i,n,r,s,o){for(var a=[0,1,1,1,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7],l=0;l1?1:0)|(e[0].do_stab?2:0);if(t.WriteByte(h),1&h&&t.WriteByte(e.length),2&h){var u=1<0&&u--,t.WriteByte(u),c(t,o,256)}for(var d=0;d0){for(l=0;l<256;l++)n[d][l]=l;e[d].do_qtab&&c(t,n[d],256)}if(e[d].pbits>0){for(l=0;l<1024;l++)r[d][l]=Math.min((1<>e[d].pshift);c(t,r[d],1024)}if(e[d].dbits>0){for(l=0;l<256;l++)a[l]>(1<>e[d].dshift)];c(t,s[d],256)}}return t}(p,f,o,a,l,h,u);return function(t,e,i,n,o,a,l,h,c,u){var d=1<0&&d--;for(var f=e.length,p=0,g=0;g0&&v.ModelEncode(t,w,x);var k=u[x],S=i[Math.min(i.length-1,_++)];o[k].fixed_len?o[k].fixed_len>0&&(y[0].ModelEncode(t,w,255&S),y[1].ModelEncode(t,w,S>>8&255),y[2].ModelEncode(t,w,S>>16&255),y[3].ModelEncode(t,w,S>>24&255),o[k].fixed_len=-1):(y[0].ModelEncode(t,w,255&S),y[1].ModelEncode(t,w,S>>8&255),y[2].ModelEncode(t,w,S>>16&255),y[3].ModelEncode(t,w,S>>24&255)),o[k].do_dedup&&process.exit(1),g=S;var C=0,A=o[k].context,T=0,I=0}var E=e[b++],M=a[k][E];m[A].ModelEncode(t,w,M),T=(T<0&&(A+=h[k][Math.min(g,1023)]<0&&(A+=c[k][Math.min(C,255)]<{var n=i(4459),r=i(594),s=i(445),o=i(5260),a=i(2881);t.exports={r4x8_uncompress:function(t,e){n.decode(t).copy(e,0,0)},r4x16_uncompress:function(t,e){r.decode(t).copy(e,0,0)},arith_uncompress:function(t,e){s.decode(t).copy(e,0,0)},fqzcomp_uncompress:function(t,e){var i=new Array;o.decode(t,i).copy(e,0,0)},tok3_uncompress:function(t,e){var i=a.decode(t,0,"\0");Buffer.from(i,"binary").copy(e,0,0)}}},9260:t=>{t.exports=class{constructor(t,e=0,i=0){0!=i?(this.buf=Buffer.allocUnsafe(i),this.length=i):(this.buf=t,this.length=t.length),this.pos=e}EOF(){return this.pos>=this.length}ReadData(t){var e=this.buf.slice(this.pos,this.pos+t);return this.pos+=t,e}ReadByte(){const t=this.buf[this.pos];return this.pos++,t}ReadChar(){const t=this.buf[this.pos];return this.pos++,String.fromCharCode(t)}ReadUint16(){return this.ReadByte()|this.ReadByte()<<8}ReadUint32(){const t=this.buf.readInt32LE(this.pos);return this.pos+=4,t}ReadString(){var t="";do{var e=this.buf[this.pos++];e&&(t+=String.fromCharCode(e))}while(e);return t}ReadUint7(){var t=0;do{var e=this.ReadByte();t=t<<7|127&e}while(128&e);return t}ReadITF8(){var t=this.buf[this.pos];return this.pos++,t>=240?(t=(15&t)<<28,t+=(this.buf[this.pos+0]<<20)+(this.buf[this.pos+1]<<12)+(this.buf[this.pos+2]<<4)+(this.buf[this.pos+3]>>4),this.pos+=4):t>=224?(t=(15&t)<<24,t+=(this.buf[this.pos+0]<<16)+(this.buf[this.pos+1]<<8)+(this.buf[this.pos+2]<<0),this.pos+=3):t>=192?(t=(31&t)<<16,t+=(this.buf[this.pos+0]<<8)+(this.buf[this.pos+1]<<0),this.pos+=2):t>=128&&(t=(63&t)<<8,t+=this.buf[this.pos],this.pos++),t}WriteByte(t){this.buf[this.pos++]=t}WriteChar(t){this.buf[this.pos++]=t.charCodeAt(0)}WriteString(t){for(var e=0;e>8&255)}WriteUint32(t){this.buf.writeInt32LE(t,this.pos),this.pos+=4}WriteUint7(t){var e=0,i=t;do{e+=7,i>>=7}while(i>0);do{e-=7,this.WriteByte((t>>e&127)+((e>0)<<7))}while(e>0)}WriteITF8(t){t<0&&(t=1+t),t<=127?this.buf[this.pos++]=t:t<=16383?(this.buf[this.pos++]=128|Math.floor(t/256),this.buf[this.pos++]=255&t):t<131071?(this.buf[this.pos++]=192|Math.floor(t/65536),this.buf[this.pos++]=255&Math.floor(t/256),this.buf[this.pos++]=255&t):t<268435455?(this.buf[this.pos++]=224|Math.floor(t/16777216),this.buf[this.pos++]=255&Math.floor(t/65536),this.buf[this.pos++]=255&Math.floor(t/256),this.buf[this.pos++]=255&t):(this.buf[this.pos++]=240|Math.floor(t/268435456),this.buf[this.pos++]=255&Math.floor(t/1048576),this.buf[this.pos++]=255&Math.floor(t/4096),this.buf[this.pos++]=255&Math.floor(t/4),this.buf[this.pos++]=15&t)}WriteByteNeg(t){this.buf[--this.pos]=t}}},4459:(t,e,i)=>{const n=i(9260);function r(t){return 4095&t}function s(t,e){for(var i=0;e>=t[i+1];)i++;return i}function o(t){for(var e=new Array(4096),i=0,n=0;n<4096;n++){for(;n>=t[i+1];)i++;e[n]=i}return e}function 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s=o(n),h=new Array(4),c=0;c<4;c++)h[c]=t.ReadUint32();var d=new Buffer.allocUnsafe(e);for(c=0;c0?(a--,s++):(s=t.ReadByte())==o+1&&(a=t.ReadByte()),o=s}while(0!=s)}(t,i,n);for(var h=new Array(256),c=0;c<256;c++)h[c]=o(n[c]);for(var d=new Array(4),f=new Array(4),p=0;p<4;p++)d[p]=t.ReadUint32(),f[p]=0;var g=new Buffer.allocUnsafe(e),m=Math.floor(e/4);for(c=0;c=0;o--)a[o%4]=c(a[o%4],u,s[t[o]],r[t[o]],12);for(o=3;o>=0;o--)h(a[o],u);var p=i.pos;return i.buf.writeInt32LE(p-9+(u.length-u.pos),1),i.buf.writeInt32LE(e,5),Buffer.concat([i.buf.slice(0,i.pos),u.buf.slice(u.pos,u.length)],i.pos+u.length-u.pos)}(t):function(t){const e=t.length;var i=new n("",0,198156);i.WriteByte(1),i.WriteUint32(0),i.WriteUint32(0);for(var r=new Array(256),s=new Array(256),o=new Array(256),a=0;a<256;a++)s[a]=new Array(256),o[a]=new Array(256);for(function(t,e,i){for(var n=0;n<256;n++){i[n]=0;for(var r=0;r<256;r++)e[n][r]=0}var s=0;for(n=0;n>2)]]++,e[0][t[2*(t.length>>2)]]++,e[0][t[3*(t.length>>2)]]++,i[0]+=3}(t,s,r),function(t,e){for(var i=0;i<256;i++)e[i]&&d(t[i])}(s,r),function(t,e,i){for(var n=0,r=0;r<256;r++)if(i[r]){if(n>0)n--;else if(t.WriteByte(r),r>0&&i[r-1]>0){for(n=r+1;n<256&&i[n];n++);n-=r+1,t.WriteByte(n)}f(t,e[r])}t.WriteByte(0)}(i,s,r),a=0;a<256;a++)if(r[a]){o[a][0]=0;for(var l=1;l<256;l++)o[a][l]=o[a][l-1]+s[a][l-1]}var u=new Array(4),p=new Array(4);for(l=0;l<4;l++)u[l]=1<<23,p[l]=0;var g=new n("",e,e),m=Math.floor(e/4),b=new Array(4),y=new Array(4);for(l=0;l<4;l++)b[l]=(l+1)*m-2,y[l]=t[b[l]+1];for(y[3]=t[e-1],a=e-2;a>4*m-2;a--)u[3]=c(u[3],g,o[t[a]][y[3]],s[t[a]][y[3]],12),y[3]=t[a];for(;b[0]>=0;)for(l=3;l>=0;l--){var v=t[b[l]];u[l]=c(u[l],g,o[v][y[l]],s[v][y[l]],12),y[l]=v,b[l]--}for(l=3;l>=0;l--)u[l]=c(u[l],g,o[0][y[l]],s[0][y[l]],12);for(a=3;a>=0;a--)h(u[a],g);var w=i.pos;return 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a=0;for(s=0;s<256;s++)o[s]&&(a>0?a--:(e[r][s]=t.ReadUint7(),0==e[r][s]&&(a=t.ReadByte())));for(b(e[r],n),i[r][0]=0,s=0;s<256;s++)i[r][s+1]=i[r][s]+e[r][s]}}(h,f,m,i);for(var y=new Array(256),v=0;v<256;v++)y[v]=o(m[v],i);for(var w=new Array(4),_=new Array(4),x=0;x<4;x++)w[x]=t.ReadUint32(),_[x]=0;var k=new Buffer.allocUnsafe(e),S=Math.floor(e/4);for(v=0;v>=1}else if(i<=4)for(o=0;o>=2;else if(i<=16)for(o=0;o>=4;return r}(S,v,w,y)),S}function f(t,e){var i=new n("",0,10);i.WriteByte(e);var r=1&e,s=8&e,o=32&e,a=64&e,l=128&e,d=e>>8;if(16&e||i.WriteUint7(t.length),s)return Buffer.concat([i.buf.slice(0,i.pos),u(0,t,d)]);var f=new Buffer.alloc(0);l&&([f,t]=function(t){for(var e=new Array(256),i=0;i<256;i++)e[i]=0;for(i=0;i0&&(r[i]=s++);if(!(s>16)){if(s<=1)var o=new Buffer.allocUnsafe(0);else if(s<=2){o=new Buffer.allocUnsafe(Math.ceil(t.length/8));var a=-1;for(i=0;i0&&(e[i]=a++,l.WriteByte(i));return l.WriteUint7(o.length),[l.buf.slice(0,l.pos),o]}}(t));var p=new Buffer.alloc(0);if(a&&([p,t]=function(t){for(var e=new Array(256),i=0;i<256;i++)e[i]=0;var r=-1;for(i=0;i0&&s++;for(s||(s=1,e[0]=1),(h=new n("",0,s+1+t.length)).WriteByte(s),i=0;i<256;i++)e[i]>0&&h.WriteByte(i);var o=new Buffer.allocUnsafe(t.length),a=0;for(i=0;i0){r=t[i];for(var l=0;i+l+1>2)]]++,e[0][t[2*(t.length>>2)]]++,e[0][t[3*(t.length>>2)]]++,i[0]+=3})(t,s,r),function(t,e,i){for(var n=0;n<256;n++)if(e[n]){var r=Math.ceil(Math.log2(e[n]));r>12&&(r=12),m(t[n],r)}}(s,r);var l=new n("",0,198156);!function(t,e,i){y(t,i);for(var n=0;n<256;n++)if(i[n])for(var r=0,s=0;s<256;s++)if(i[s])if(r)r--;else if(t.WriteUint7(e[n][s]),!e[n][s]){for(var o=s+1;o<256;o++)if(i[o]){if(0!=e[n][o])break;r++}t.WriteByte(r)}}(l,s,r);var u=v(l.buf.slice(0,l.pos));for(u.length>0,1.05*e+100>>0),w=Math.floor(e/4),_=new Array(4),x=new 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Buffer.allocUnsafe(e);for(c=0;c2?t[a]-=i-r:i!=r&&(s=r/i,l=1)}while(l)}function b(t,e){for(var i=0,n=0;n<256;n++)i+=t[n];if(0!=i&&i!=1<0)i--;else if(t.WriteByte(n),n>0&&e[n-1]>0){for(i=n+1;i<256&&e[i];i++);i-=n+1,t.WriteByte(i)}t.WriteByte(0)}function v(t){const e=t.length;var i=new n("",0,780),r=new Array(256);!function(t,e){for(var i=0;i<256;i++)e[i]=0;for(i=0;i12&&(s=12),m(r,s),function(t,e){y(t,e);for(var i=0;i<256;i++)e[i]&&t.WriteUint7(e[i])}(i,r),m(r,12);var o=new Array(256);o[0]=0;for(var a=1;a<256;a++)o[a]=o[a-1]+r[a-1];var l=new Array(4);for(a=0;a<4;a++)l[a]=32768;var u=new n("",1.05*e+100>>0,1.05*e+100>>0);for(a=e-1;a>=0;a--)l[a%4]=c(l[a%4],u,o[t[a]],r[t[a]],12);for(a=3;a>=0;a--)h(l[a],u);return Buffer.concat([i.buf.slice(0,i.pos),u.buf.slice(u.pos,u.length)],i.pos+u.length-u.pos)}t.exports={decode:function(t){return d(new n(t),0)},encode:f}},2881:(t,e,i)=>{const n=i(9260),r=i(594);var s=new(i(445));function o(t,e){for(var i=t+"";i.length>0)+t[a][8].ReadByte();break;case 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0===t.avail_out&&(r.last_flush=-1),0;if(2===x&&(1===e?s._tr_align(r):5!==e&&(s._tr_stored_block(r,0,0,!1),3===e&&(b(r.head),0===r.lookahead&&(r.strstart=0,r.block_start=0,r.insert=0))),y(t),0===t.avail_out))return r.last_flush=-1,0}return 4!==e?0:r.wrap<=0?1:(2===r.wrap?(w(r,255&t.adler),w(r,t.adler>>8&255),w(r,t.adler>>16&255),w(r,t.adler>>24&255),w(r,255&t.total_in),w(r,t.total_in>>8&255),w(r,t.total_in>>16&255),w(r,t.total_in>>24&255)):(_(r,t.adler>>>16),_(r,65535&t.adler)),y(t),r.wrap>0&&(r.wrap=-r.wrap),0!==r.pending?0:1)},e.deflateEnd=function(t){var e;return t&&t.state?42!==(e=t.state.status)&&69!==e&&73!==e&&91!==e&&e!==d&&e!==f&&e!==p?g(t,h):(t.state=null,e===f?g(t,-3):0):h},e.deflateSetDictionary=function(t,e){var i,n,s,a,l,c,u,d,f=e.length;if(!t||!t.state)return h;if(2===(a=(i=t.state).wrap)||1===a&&42!==i.status||i.lookahead)return h;for(1===a&&(t.adler=o(t.adler,e,f,0)),i.wrap=0,f>=i.w_size&&(0===a&&(b(i.head),i.strstart=0,i.block_start=0,i.insert=0),d=new 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distance too far back",i.mode=30;break t}if(k=0,S=d,0===u){if(k+=h-w,w<_){_-=w;do{A[s++]=d[k++]}while(--w);k=s-x,S=A}}else if(u2;)A[s++]=S[k++],A[s++]=S[k++],A[s++]=S[k++],_-=3;_&&(A[s++]=S[k++],_>1&&(A[s++]=S[k++]))}else{k=s-x;do{A[s++]=A[k++],A[s++]=A[k++],A[s++]=A[k++],_-=3}while(_>2);_&&(A[s++]=A[k++],_>1&&(A[s++]=A[k++]))}break}}break}}while(n>3,f&=(1<<(p-=_<<3))-1,t.next_in=n,t.next_out=s,t.avail_in=n{var n=i(4236),r=i(6069),s=i(2869),o=i(4264),a=i(9241),l=-2,h=12,c=30;function u(t){return(t>>>24&255)+(t>>>8&65280)+((65280&t)<<8)+((255&t)<<24)}function d(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new n.Buf16(320),this.work=new n.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function f(t){var e;return t&&t.state?(e=t.state,t.total_in=t.total_out=e.total=0,t.msg="",e.wrap&&(t.adler=1&e.wrap),e.mode=1,e.last=0,e.havedict=0,e.dmax=32768,e.head=null,e.hold=0,e.bits=0,e.lencode=e.lendyn=new n.Buf32(852),e.distcode=e.distdyn=new n.Buf32(592),e.sane=1,e.back=-1,0):l}function p(t){var e;return t&&t.state?((e=t.state).wsize=0,e.whave=0,e.wnext=0,f(t)):l}function g(t,e){var i,n;return t&&t.state?(n=t.state,e<0?(i=0,e=-e):(i=1+(e>>4),e<48&&(e&=15)),e&&(e<8||e>15)?l:(null!==n.window&&n.wbits!==e&&(n.window=null),n.wrap=i,n.wbits=e,p(t))):l}function m(t,e){var i,n;return t?(n=new d,t.state=n,n.window=null,0!==(i=g(t,e))&&(t.state=null),i):l}var b,y,v=!0;function w(t){if(v){var e;for(b=new n.Buf32(512),y=new n.Buf32(32),e=0;e<144;)t.lens[e++]=8;for(;e<256;)t.lens[e++]=9;for(;e<280;)t.lens[e++]=7;for(;e<288;)t.lens[e++]=8;for(a(1,t.lens,0,288,b,0,t.work,{bits:9}),e=0;e<32;)t.lens[e++]=5;a(2,t.lens,0,32,y,0,t.work,{bits:5}),v=!1}t.lencode=b,t.lenbits=9,t.distcode=y,t.distbits=5}function _(t,e,i,r){var s,o=t.state;return null===o.window&&(o.wsize=1<=o.wsize?(n.arraySet(o.window,e,i-o.wsize,o.wsize,0),o.wnext=0,o.whave=o.wsize):((s=o.wsize-o.wnext)>r&&(s=r),n.arraySet(o.window,e,i-r,s,o.wnext),(r-=s)?(n.arraySet(o.window,e,i-r,r,0),o.wnext=r,o.whave=o.wsize):(o.wnext+=s,o.wnext===o.wsize&&(o.wnext=0),o.whave>>8&255,i.check=s(i.check,P,2,0),y=0,v=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&y)<<8)+(y>>8))%31){t.msg="incorrect header check",i.mode=c;break}if(8!=(15&y)){t.msg="unknown compression method",i.mode=c;break}if(v-=4,B=8+(15&(y>>>=4)),0===i.wbits)i.wbits=B;else if(B>i.wbits){t.msg="invalid window size",i.mode=c;break}i.dmax=1<>8&1),512&i.flags&&(P[0]=255&y,P[1]=y>>>8&255,i.check=s(i.check,P,2,0)),y=0,v=0,i.mode=3;case 3:for(;v<32;){if(0===m)break t;m--,y+=d[p++]<>>8&255,P[2]=y>>>16&255,P[3]=y>>>24&255,i.check=s(i.check,P,4,0)),y=0,v=0,i.mode=4;case 4:for(;v<16;){if(0===m)break t;m--,y+=d[p++]<>8),512&i.flags&&(P[0]=255&y,P[1]=y>>>8&255,i.check=s(i.check,P,2,0)),y=0,v=0,i.mode=5;case 5:if(1024&i.flags){for(;v<16;){if(0===m)break t;m--,y+=d[p++]<>>8&255,i.check=s(i.check,P,2,0)),y=0,v=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((S=i.length)>m&&(S=m),S&&(i.head&&(B=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,d,p,S,B)),512&i.flags&&(i.check=s(i.check,d,S,p)),m-=S,p+=S,i.length-=S),i.length))break t;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===m)break t;S=0;do{B=d[p+S++],i.head&&B&&i.length<65536&&(i.head.name+=String.fromCharCode(B))}while(B&&S>9&1,i.head.done=!0),t.adler=i.check=0,i.mode=h;break;case 10:for(;v<32;){if(0===m)break t;m--,y+=d[p++]<>>=7&v,v-=7&v,i.mode=27;break}for(;v<3;){if(0===m)break t;m--,y+=d[p++]<>>=1)){case 0:i.mode=14;break;case 1:if(w(i),i.mode=20,6===e){y>>>=2,v-=2;break t}break;case 2:i.mode=17;break;case 3:t.msg="invalid block type",i.mode=c}y>>>=2,v-=2;break;case 14:for(y>>>=7&v,v-=7&v;v<32;){if(0===m)break t;m--,y+=d[p++]<>>16^65535)){t.msg="invalid stored block lengths",i.mode=c;break}if(i.length=65535&y,y=0,v=0,i.mode=15,6===e)break t;case 15:i.mode=16;case 16:if(S=i.length){if(S>m&&(S=m),S>b&&(S=b),0===S)break t;n.arraySet(f,d,p,S,g),m-=S,p+=S,b-=S,g+=S,i.length-=S;break}i.mode=h;break;case 17:for(;v<14;){if(0===m)break t;m--,y+=d[p++]<>>=5,v-=5,i.ndist=1+(31&y),y>>>=5,v-=5,i.ncode=4+(15&y),y>>>=4,v-=4,i.nlen>286||i.ndist>30){t.msg="too many length or distance symbols",i.mode=c;break}i.have=0,i.mode=18;case 18:for(;i.have>>=3,v-=3}for(;i.have<19;)i.lens[z[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,F={bits:i.lenbits},N=a(0,i.lens,0,19,i.lencode,0,i.work,F),i.lenbits=F.bits,N){t.msg="invalid code lengths set",i.mode=c;break}i.have=0,i.mode=19;case 19:for(;i.have>>16&255,E=65535&D,!((T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>>=T,v-=T,i.lens[i.have++]=E;else{if(16===E){for(O=T+2;v>>=T,v-=T,0===i.have){t.msg="invalid bit length repeat",i.mode=c;break}B=i.lens[i.have-1],S=3+(3&y),y>>>=2,v-=2}else if(17===E){for(O=T+3;v>>=T)),y>>>=3,v-=3}else{for(O=T+7;v>>=T)),y>>>=7,v-=7}if(i.have+S>i.nlen+i.ndist){t.msg="invalid bit length repeat",i.mode=c;break}for(;S--;)i.lens[i.have++]=B}}if(i.mode===c)break;if(0===i.lens[256]){t.msg="invalid code -- missing end-of-block",i.mode=c;break}if(i.lenbits=9,F={bits:i.lenbits},N=a(1,i.lens,0,i.nlen,i.lencode,0,i.work,F),i.lenbits=F.bits,N){t.msg="invalid literal/lengths set",i.mode=c;break}if(i.distbits=6,i.distcode=i.distdyn,F={bits:i.distbits},N=a(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,F),i.distbits=F.bits,N){t.msg="invalid distances set",i.mode=c;break}if(i.mode=20,6===e)break t;case 20:i.mode=21;case 21:if(m>=6&&b>=258){t.next_out=g,t.avail_out=b,t.next_in=p,t.avail_in=m,i.hold=y,i.bits=v,o(t,k),g=t.next_out,f=t.output,b=t.avail_out,p=t.next_in,d=t.input,m=t.avail_in,y=i.hold,v=i.bits,i.mode===h&&(i.back=-1);break}for(i.back=0;I=(D=i.lencode[y&(1<>>16&255,E=65535&D,!((T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>M)])>>>16&255,E=65535&D,!(M+(T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>>=M,v-=M,i.back+=M}if(y>>>=T,v-=T,i.back+=T,i.length=E,0===I){i.mode=26;break}if(32&I){i.back=-1,i.mode=h;break}if(64&I){t.msg="invalid literal/length code",i.mode=c;break}i.extra=15&I,i.mode=22;case 22:if(i.extra){for(O=i.extra;v>>=i.extra,v-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;I=(D=i.distcode[y&(1<>>16&255,E=65535&D,!((T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>M)])>>>16&255,E=65535&D,!(M+(T=D>>>24)<=v);){if(0===m)break t;m--,y+=d[p++]<>>=M,v-=M,i.back+=M}if(y>>>=T,v-=T,i.back+=T,64&I){t.msg="invalid distance code",i.mode=c;break}i.offset=E,i.extra=15&I,i.mode=24;case 24:if(i.extra){for(O=i.extra;v>>=i.extra,v-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){t.msg="invalid distance too far back",i.mode=c;break}i.mode=25;case 25:if(0===b)break t;if(S=k-b,i.offset>S){if((S=i.offset-S)>i.whave&&i.sane){t.msg="invalid distance too far back",i.mode=c;break}S>i.wnext?(S-=i.wnext,C=i.wsize-S):C=i.wnext-S,S>i.length&&(S=i.length),A=i.window}else A=f,C=g-i.offset,S=i.length;S>b&&(S=b),b-=S,i.length-=S;do{f[g++]=A[C++]}while(--S);0===i.length&&(i.mode=21);break;case 26:if(0===b)break t;f[g++]=i.length,b--,i.mode=21;break;case 27:if(i.wrap){for(;v<32;){if(0===m)break t;m--,y|=d[p++]<{var n=i(4236),r=[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],s=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],o=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],a=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64];t.exports=function(t,e,i,l,h,c,u,d){var f,p,g,m,b,y,v,w,_,x=d.bits,k=0,S=0,C=0,A=0,T=0,I=0,E=0,M=0,R=0,L=0,B=null,N=0,F=new n.Buf16(16),O=new n.Buf16(16),D=null,P=0;for(k=0;k<=15;k++)F[k]=0;for(S=0;S=1&&0===F[A];A--);if(T>A&&(T=A),0===A)return h[c++]=20971520,h[c++]=20971520,d.bits=1,0;for(C=1;C0&&(0===t||1!==A))return-1;for(O[1]=0,k=1;k<15;k++)O[k+1]=O[k]+F[k];for(S=0;S852||2===t&&R>592)return 1;for(;;){v=k-E,u[S]y?(w=D[P+u[S]],_=B[N+u[S]]):(w=96,_=0),f=1<>E)+(p-=f)]=v<<24|w<<16|_|0}while(0!==p);for(f=1<>=1;if(0!==f?(L&=f-1,L+=f):L=0,S++,0==--F[k]){if(k===A)break;k=e[i+u[S]]}if(k>T&&(L&m)!==g){for(0===E&&(E=T),b+=C,M=1<<(I=k-E);I+E852||2===t&&R>592)return 1;h[g=L&m]=T<<24|I<<16|b-c|0}}return 0!==L&&(h[b+L]=k-E<<24|64<<16|0),d.bits=T,0}},8898:t=>{t.exports={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"}},342:(t,e,i)=>{var n=i(4236);function r(t){for(var e=t.length;--e>=0;)t[e]=0}var s=[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],o=[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],a=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],l=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],h=new Array(576);r(h);var c=new Array(60);r(c);var u=new Array(512);r(u);var d=new Array(256);r(d);var f=new Array(29);r(f);var p,g,m,b=new Array(30);function y(t,e,i,n,r){this.static_tree=t,this.extra_bits=e,this.extra_base=i,this.elems=n,this.max_length=r,this.has_stree=t&&t.length}function v(t,e){this.dyn_tree=t,this.max_code=0,this.stat_desc=e}function w(t){return t<256?u[t]:u[256+(t>>>7)]}function _(t,e){t.pending_buf[t.pending++]=255&e,t.pending_buf[t.pending++]=e>>>8&255}function x(t,e,i){t.bi_valid>16-i?(t.bi_buf|=e<>16-t.bi_valid,t.bi_valid+=i-16):(t.bi_buf|=e<>>=1,i<<=1}while(--e>0);return i>>>1}function C(t,e,i){var n,r,s=new Array(16),o=0;for(n=1;n<=15;n++)s[n]=o=o+i[n-1]<<1;for(r=0;r<=e;r++){var a=t[2*r+1];0!==a&&(t[2*r]=S(s[a]++,a))}}function A(t){var e;for(e=0;e<286;e++)t.dyn_ltree[2*e]=0;for(e=0;e<30;e++)t.dyn_dtree[2*e]=0;for(e=0;e<19;e++)t.bl_tree[2*e]=0;t.dyn_ltree[512]=1,t.opt_len=t.static_len=0,t.last_lit=t.matches=0}function T(t){t.bi_valid>8?_(t,t.bi_buf):t.bi_valid>0&&(t.pending_buf[t.pending++]=t.bi_buf),t.bi_buf=0,t.bi_valid=0}function I(t,e,i,n){var r=2*e,s=2*i;return 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e of this.oldCache.keys())this.cache.has(e)||t++;return this._size+t}}var Vu={ALIGNMENT_MATCH:"M",INSERT:"I",DELETE:"D",SKIP:"N",CLIP_SOFT:"S",CLIP_HARD:"H",PAD:"P",SEQUENCE_MATCH:"=",SEQUENCE_MISMATCH:"X"};const Hu=function(t,e){this.config=t,this.genome=e,this.url=t.url,this.filter=new wu(t.filter),this.readGroupSetIds=t.readGroupSetIds,this.authKey=t.authKey,this.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,this.samplingDepth=void 0===t.samplingDepth?1e3:t.samplingDepth,t.viewAsPairs?this.pairsSupported=!0:this.pairsSupported=void 0===t.pairsSupported||t.pairsSupported};Hu.prototype.readAlignments=function(t,e,i){const n=this.genome,r=this;return(r.chrAliasTable?Promise.resolve(r.chrAliasTable):r.readMetadata().then((function(t){if(r.chrAliasTable={},n&&t.readGroups&&t.readGroups.length>0){var e=t.readGroups[0].referenceSetId;return e?oc({url:r.url+"/references/search",body:{referenceSetId:e},decode:function(t){return t.references}}).then((function(t){return t.forEach((function(t){var e=t.name,i=n.getChromosomeName(e);r.chrAliasTable[i]=e})),r.chrAliasTable})):(function(t,e){var i;if("461916304629"===e||"337315832689"===e){for(i=1;i<23;i++)t["chr"+i]=i;t.chrX="X",t.chrY="Y",t.chrM="MT"}}(r.chrAliasTable,r.config.datasetId),r.chrAliasTable)}return r.chrAliasTable}))).then((function(n){var o=n.hasOwnProperty(t)?n[t]:t;return oc({url:r.url+"/reads/search",body:{readGroupSetIds:[r.readGroupSetIds],referenceName:o,start:e,end:i,pageSize:"10000"},decode:s,results:new nu(t,e,i,r.config)})}));function s(t){var e,i,s,o,a,l=t.alignments,h=l.length,c=[];for(e=0;e0;if(s.packedAlignmentRows=eu(o,s.start,s.end,r),this.alignmentContainer=s,a){const e=await n.sequence.getSequence(t,s.start,s.end);if(e)return s.coverageMap.refSeq=e,s.sequence=e,s;console.error("No sequence for: "+t+":"+s.start+"-"+s.end)}return s}}function $u(t,e,i){var n,r,s,o,a,l,h,c={font:"normal 10px 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h=e.match(/([\-\d\.e]+)/g).map(Number),c=Zu(h,4),u=c[0],d=c[1],f=c[2],p=c[3];void 0===p&&(p=1),s.rgba=[u,d,f,p]}else e.startsWith("#")?s.rgba=t.hexToRgb(e):s.rgba=t.nameToRgb(e)||t.hexToRgb(e)}(o.toLowerCase())}else this.rgba=[e,i,n,void 0===r?1:r]}return Gu(t,[{key:"printRGB",value:function(t){var e=(t?this.rgba:this.rgba.slice(0,3)).map((function(t,e){return Qu(t,3===e?3:0)}));return t?"rgba("+e+")":"rgb("+e+")"}},{key:"printHSL",value:function(t){var e=[360,100,100,1],i=["","%","%",""],n=(t?this.hsla:this.hsla.slice(0,3)).map((function(t,n){return Qu(t*e[n],3===n?3:1)+i[n]}));return t?"hsla("+n+")":"hsl("+n+")"}},{key:"printHex",value:function(t){var e=this.hex;return t?e:e.substring(0,7)}},{key:"rgba",get:function(){if(this._rgba)return this._rgba;if(!this._hsla)throw new Error("No color is set");return this._rgba=t.hslToRgb(this._hsla)},set:function(t){3===t.length&&(t[3]=1),this._rgba=t,this._hsla=null}},{key:"rgbString",get:function(){return this.printRGB()}},{key:"rgbaString",get:function(){return this.printRGB(!0)}},{key:"hsla",get:function(){if(this._hsla)return this._hsla;if(!this._rgba)throw new Error("No color is set");return this._hsla=t.rgbToHsl(this._rgba)},set:function(t){3===t.length&&(t[3]=1),this._hsla=t,this._rgba=null}},{key:"hslString",get:function(){return this.printHSL()}},{key:"hslaString",get:function(){return this.printHSL(!0)}},{key:"hex",get:function(){return"#"+this.rgba.map((function(t,e){return e<3?t.toString(16):Math.round(255*t).toString(16)})).map((function(t){return t.padStart(2,"0")})).join("")},set:function(e){this.rgba=t.hexToRgb(e)}}],[{key:"hexToRgb",value:function(t){var e=(t.startsWith("#")?t.slice(1):t).replace(/^(\w{3})$/,"$1F").replace(/^(\w)(\w)(\w)(\w)$/,"$1$1$2$2$3$3$4$4").replace(/^(\w{6})$/,"$1FF");if(!e.match(/^([0-9a-fA-F]{8})$/))throw new Error("Unknown hex color; "+t);var i=e.match(/^(\w\w)(\w\w)(\w\w)(\w\w)$/).slice(1).map((function(t){return parseInt(t,16)}));return 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r=i.parent;if(r&&i.popup&&!this._popupInited){var s=function(t){return e.openHandler(t)};this._events.add(r,"click",s),sd(this._events,r,[" ","Spacebar","Enter"],s),this._popupInited=!0}else t.parent&&!i.popup&&this.show()}}},{key:"openHandler",value:function(t){if(this.show()){t&&t.preventDefault(),this.settings.parent.style.pointerEvents="none";var e=t&&t.type===td?this._domEdit:this.domElement;setTimeout((function(){return e.focus()}),100),this.onOpen&&this.onOpen(this.colour)}}},{key:"closeHandler",value:function(t){var e=t&&t.type,i=!1;if(t)if(e===ed||e===id){var n=(this.__containedEvent||0)+100;t.timeStamp>n&&(i=!0)}else rd(t),i=!0;else 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.picker_sl::before{content:"";display:block;padding-bottom:100%}.layout_default .picker_editor{order:1;width:6.5rem}.layout_default .picker_editor input{width:100%;height:100%}.layout_default .picker_sample{order:1;flex:1 1 auto}.layout_default .picker_done,.layout_default .picker_cancel{order:1}.picker_wrapper{box-sizing:border-box;background:#f2f2f2;box-shadow:0 0 0 1px silver;cursor:default;font-family:sans-serif;color:#444;pointer-events:auto}.picker_wrapper:focus{outline:none}.picker_wrapper button,.picker_wrapper input{box-sizing:border-box;border:none;box-shadow:0 0 0 1px silver;outline:none}.picker_wrapper button:focus,.picker_wrapper button:active,.picker_wrapper input:focus,.picker_wrapper input:active{box-shadow:0 0 2px 1px #1e90ff}.picker_wrapper button{padding:.4em .6em;cursor:pointer;background-color:#f5f5f5;background-image:linear-gradient(0deg, gainsboro, transparent)}.picker_wrapper button:active{background-image:linear-gradient(0deg, transparent, gainsboro)}.picker_wrapper button:hover{background-color:#fff}.picker_selector{position:absolute;z-index:1;display:block;-webkit-transform:translate(-50%, -50%);transform:translate(-50%, -50%);border:2px solid #fff;border-radius:100%;box-shadow:0 0 3px 1px #67b9ff;background:currentColor;cursor:pointer}.picker_slider .picker_selector{border-radius:2px}.picker_hue{position:relative;background-image:linear-gradient(90deg, red, yellow, lime, cyan, blue, magenta, red);box-shadow:0 0 0 1px silver}.picker_sl{position:relative;box-shadow:0 0 0 1px silver;background-image:linear-gradient(180deg, white, rgba(255, 255, 255, 0) 50%),linear-gradient(0deg, black, rgba(0, 0, 0, 0) 50%),linear-gradient(90deg, #808080, rgba(128, 128, 128, 0))}.picker_alpha,.picker_sample{position:relative;background:linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0/2em 2em,linear-gradient(45deg, lightgrey 25%, white 25%, white 75%, lightgrey 75%) 1em 1em/2em 2em;box-shadow:0 0 0 1px silver}.picker_alpha .picker_selector,.picker_sample .picker_selector{background:none}.picker_editor input{font-family:monospace;padding:.2em .4em}.picker_sample::before{content:"";position:absolute;display:block;width:100%;height:100%;background:currentColor}.picker_arrow{position:absolute;z-index:-1}.picker_wrapper.popup{position:absolute;z-index:2;margin:1.5em}.picker_wrapper.popup,.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{background:#f2f2f2;box-shadow:0 0 10px 1px rgba(0,0,0,.4)}.picker_wrapper.popup .picker_arrow{width:3em;height:3em;margin:0}.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{content:"";display:block;position:absolute;top:0;left:0;z-index:-99}.picker_wrapper.popup .picker_arrow::before{width:100%;height:100%;-webkit-transform:skew(45deg);transform:skew(45deg);-webkit-transform-origin:0 100%;transform-origin:0 100%}.picker_wrapper.popup .picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(ad),od.StyleElement=ad;const hd={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};class cd{constructor(t){this.tracks=[],this.chordSets=[]}addChordSet(t){this.chordSets=this.chordSets.filter((e=>e.name!==t.name)),this.chordSets.push(t);let e=this.tracks.find((e=>t.trackName===e.name));e&&(e.chordSets=e.chordSets.filter((e=>e.name!==t.name)),e.chordSets.push(t)),e||(e=new ud(t),this.tracks.push(e))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(t){return this.tracks.find((e=>t===e.name))}getChordSet(t){return this.chordSets.find((e=>t===e.name))}}class ud{constructor(t){this.name=t.trackName,this.color=t.trackColor,this.visible=!0,this.chordSets=[t],this.id=("0000"+(Math.random()*Math.pow(36,4)<<0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const t=[];for(let e of this.chordSets)for(let i of e.chords)t.push(i);return t}}const dd=Math.exp(5);class fd{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(t,e){if(e=e||{},this.config=e,fd.isInstalled()){this.parent=t,this.groupByTrack=!0===e.groupByTrack,this.chordManager=new cd(e);const i=document.createElement("div");i.className="igv-circview-container",t.appendChild(i),this.createControls(i),this.resetControlPanel();const n=document.createElement("div");n.className="igv-circview-circular-genome-view",i.appendChild(n),this.container=n,e.assembly&&this.setAssembly(e.assembly),this.width=e.width||500,this.height=e.height||500,this.setSize(this.width,this.height)}else console.error("JBrowse circular view is not installed")}createControls(t){const e=document.createElement("div");e.className="igv-circview-toolbar",t.appendChild(e),this.toolbar=e;const i=document.createElement("div");i.className="igv-circview-track-panel",t.appendChild(i),this.controlPanel=i,this.controlPanel.style.display="none";const n=document.createElement("div");n.className="igv-circview-toolbar-button-container",this.toolbar.appendChild(n),this.showControlsButton=document.createElement("div"),this.showControlsButton.className="igv-circview-button",n.appendChild(this.showControlsButton),this.showControlsButton.innerText="none"===this.controlPanel.style.display?"Show Controls":"Hide Controls",this.showControlsButton.addEventListener("click",(t=>{this.controlPanel.querySelectorAll("div").length>0&&("none"===this.controlPanel.style.display?(this.controlPanel.style.display="flex",t.target.innerText="Hide Controls"):(this.controlPanel.style.display="none",t.target.innerText="Show Controls"))}));let r=document.createElement("div");r.className="igv-circview-button",n.appendChild(r),r.innerText="Clear All",r.addEventListener("click",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(r=document.createElement("div"),r.className="igv-circview-button",n.appendChild(r),r.innerText="Close",r.addEventListener("click",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML="",this.controlPanel.appendChild(this.createGroupByCB());const t=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let e of t)this.addToControlPanel(e)}createGroupByCB(){const t=document.createElement("input");t.type="checkbox",t.id="groupByCB",t.style.width="1.4em",t.style.height="1.4em",t.checked=this.groupByTrack,t.onclick=t=>{this.groupByTrack=t.target.checked,this.resetControlPanel(),this.render()};const e=document.createElement("label");e.for="groupByCB",e.innerText="Group by track",e.style.color="black",e.style.paddingLeft="10px";const i=document.createElement("div");return i.style.width="100%",i.style.paddingTop="5px",i.style.paddingBottom="5px",i.style.background="rgb(216, 230, 234)",i.appendChild(t),i.appendChild(e),i}addToControlPanel(t){const e=document.createElement("div");this.controlPanel.appendChild(e);const i=document.createElement("div");i.className="igv-circview-button",e.appendChild(i),i.innerText=!0===t.visible?"Hide":"Show",i.addEventListener("click",(e=>{!0===t.visible?(this.hideChordSet(t.name),e.target.innerText="Show"):(this.showChordSet(t.name),e.target.innerText="Hide")}));const n=document.createElement("input"),r=t=>200*Math.log(t*dd),s=document.createElement("div");s.className="igv-circview-button",s.innerHTML="    ",e.appendChild(s),s.style.backgroundColor=pd(t.color,1);const o={parent:s,popup:"right",editorFormat:"rgb",color:t.color,onChange:({rgbaString:e})=>{s.style.backgroundColor=pd(e,1),this.setColor(t.name,e),n.value=r(gd(t.color))}},a=new od(o);n.setAttribute("title","Adjust transparency of arcs"),n.type="range",n.style.width="100px",n.style.marginRight="10px",n.setAttribute("class","range"),n.setAttribute("min","0"),n.setAttribute("max","1000"),n.value=r(gd(t.color)),n.oninput=()=>{const e=(i=n.value,Math.exp(i/200)/dd);var i;this.setColor(t.name,pd(t.color,e)),a.setColor(t.color)},e.appendChild(n);const l=document.createElement("div");l.style.color="black",e.appendChild(l),l.innerText=l.title=t.name}setAssembly(t){const e=this.genomeId||yd();if(this.genomeId===e)return;this.chordManager.clearChords(),this.genomeId=e,this.chrNames=new Set(t.chromosomes.map((t=>md(t.name))));const i=[],n=[];for(let e of t.chromosomes){const t=md(e.name);n.push(e.color||ld(t)),i.push({refName:t,uniqueId:t,start:0,end:e.bpLength})}this.assembly={name:t.name,sequence:{trackId:e,type:"ReferenceSequenceTrack",adapter:{type:"FromConfigSequenceAdapter",features:i}},refNameColors:n},this.render()}addChords(t,e={}){const i=e.name||e.track||"*",n=i.split(" ")[0].replaceAll("%20"," "),r={name:i.replaceAll("%20"," "),trackName:n,chords:t,color:e.color||"black",trackColor:e.trackColor||e.color||"black",visible:!0,id:e.id||yd()};this.chordManager.addChordSet(r),this.resetControlPanel(),this.render()}setSize(t,e){if(e=e||t,this.width=t,this.height=e,this.viewState){const i=this.viewState.session.view;i.setWidth(t),i.setHeight(e),i.setBpPerPx(i.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display="block"}hide(){this.parent.style.display="none"}get visible(){return"none"!==this.parent.style.display}set visible(t){this.parent.style.display=t?"block":"none"}hideChordSet(t){let e=this.getChordSet(t);e?(e.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(t){let e=this.getChordSet(t);e?(e.visible=!0,this.render()):console.warn(`No track with name: ${t}`)}deleteTrack(t){let e=this.tracks.findIndex((e=>t===e.name));e>=0&&this.tracks.splice(e,1),this.render()}getChordSet(t){return this.groupByTrack?this.chordManager.getTrack(t):this.chordManager.getChordSet(t)}setColor(t,e){const i=this.getChordSet(t);if(i){i.color=e;const t=i.id;for(let i of this.viewState.config.tracks)if(t===i.trackId){i.displays[0].renderer.strokeColor.set(e);break}}}render(){const{createViewState:t,JBrowseCircularGenomeView:e}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const i=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((t=>t.visible)),n=[],r=[];for(let t of i)n.push({trackId:t.id,name:t.name,assemblyNames:["forIGV"],type:"VariantTrack",adapter:{type:"FromConfigAdapter",features:t.chords}}),r.push(t.color);this.viewState=t({assembly:this.assembly,tracks:n});for(let t=0;t div {\n margin: 4px;\n}\n\n.igv-circview-track-panel {\n z-index: 1024;\n position: absolute;\n top: 33px;\n left: 0;\n width: 100%;\n height: fit-content;\n border-bottom-style: solid;\n border-bottom-color: dimgray;\n border-bottom-width: thin;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n}\n.igv-circview-track-panel > div {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-circview-track-panel > div > div {\n margin: 4px;\n}\n\n.igv-circview-swatch-button {\n cursor: pointer;\n padding: 5px;\n width: 8px;\n height: 8px;\n border: 1px solid #8d8b8b;\n border-radius: 16px;\n}\n\n.igv-circview-button {\n cursor: pointer;\n padding: 5px;\n color: #444;\n vertical-align: middle;\n text-align: center;\n font-family: "Open Sans", sans-serif;\n font-size: 12px;\n border: 1px solid #8d8b8b;\n border-radius: 4px;\n background: #efefef;\n box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\n}\n\n.igv-circview-button:hover {\n background: #efefef;\n box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n.igv-circview-button:active {\n color: #007bff;\n box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\n}\n\n/*# sourceMappingURL=circular-view.css.map */\n',document.head.insertBefore(t,document.head.childNodes[document.head.childNodes.length-1])}()}const vd=t=>t.startsWith("chr")?t.substring(3):t;function wd(t){const e=[],i=[];for(let n of t.wgChromosomeNames){const r=t.getChromosome(n);i.push(Zd(r.name)),e.push({name:r.name,bpLength:r.bpLength})}return e}function _d(t,e,i,n){const r=e.color||"rgb(0,0,255)",s=xo.addAlpha("all"===i.chr?r:Zd(i.chr),n),o=xo.addAlpha(r,n),a=e.name.replaceAll(" ","%20"),l="all"===i.chr?a:`${a} ${i.chr}:${i.start}-${i.end}`;e.browser.circularView.addChords(t,{track:l,color:s,trackColor:o}),e.browser.circularViewVisible||(e.browser.circularViewVisible=!0)}class xd{constructor(t,{minTLENPercentile:e,maxTLENPercentile:i}){this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===e?.1:e,this.up=void 0===i?99.5:i,this.isizes=[],this.compute(t)}compute(t){for(let n of t)if(n.isProperPair()){var e=Math.abs(n.fragmentLength);this.sumF+=e,this.sumF2+=e*e,this.isizes.push(e);var i=n.pairOrientation;if("string"==typeof i&&4===i.length)switch(""+i.charAt(0)+i.charAt(2)){case"FF":case"RR":this.ffCount++;break;case"FR":this.frCount++;break;case"RF":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation="ff":this.frCount/this.totalCount>.9?this.orienation="fr":this.rfCount/this.totalCount>.9&&(this.orienation="rf"),this.minTLEN=0===this.lp?0:kd(this.isizes,this.lp),this.maxTLEN=kd(this.isizes,this.up)}}function kd(t,e){if(0!==t.length){var i=Math.floor(t.length*(e/100));return t.sort((function(t,e){return t-e})),t[i]}}const Sd={getTissueInfo:function(t,e){let i=(e=e||"https://gtexportal.org/rest/v1")+"/dataset/tissueInfo?datasetId="+(t=t||"gtex_v8");return zo.loadJson(i,{})},trackConfiguration:function(t,e){return{type:"eqtl",sourceType:"gtex-ws",url:(e=e||"https://gtexportal.org/rest/v1")+"/association/singleTissueEqtlByLocation",tissueSiteDetailId:t.tissueSiteDetailId,name:t.tissueSiteDetailId.split("_").join(" "),visibilityWindow:25e4}}};function Cd(t,e,i){let n=(t.start-e)/i,r=(t.end-e)/i,s=r-n;return s<3&&(s=3,n-=1.5),{px:n,px1:r,pw:s}}function Ad(t,e,i,n,r,s){try{r.save(),r.fillStyle=this.color,r.strokeStyle=this.color;const n=this.getColorForFeature(t);let o,a;r.fillStyle=n,r.strokeStyle=n,"SQUISHED"===this.displayMode&&void 0!==t.row?(o=this.featureHeight/2,a=this.margin+this.squishedRowHeight*t.row):"EXPANDED"===this.displayMode&&void 0!==t.row?(o=this.featureHeight,a=this.margin+this.expandedRowHeight*t.row):(o=this.featureHeight,a=this.margin);const l=s.pixelWidth,h=a+o/2,c=o/2,u=h-c/2,d=t.exons?t.exons.length:0,f=Cd(t,e,i),p=this.arrowSpacing,g="+"===t.strand?1:"-"===t.strand?-1:0;if(0===d){const t=Math.max(0,f.px),e=Math.min(l,f.px1),i=e-t;if(r.fillRect(t,a,i,o),0!==g){r.fillStyle="white",r.strokeStyle="white";for(let i=t+p/2;il)break;if(d.utr)r.fillRect(m,u,y,c);else if(d.cdStart&&(f=Math.round((d.cdStart-e)/i),r.fillRect(m,u,f-m,c),y-=f-m,m=f),d.cdEnd&&(f=Math.round((d.cdEnd-e)/i),r.fillRect(f,u,b-f,c),y-=b-f,b=f),y=Math.max(y,1),r.fillRect(m,a,y,o),y>p+5&&0!==g){r.fillStyle="white",r.strokeStyle="white";for(let t=m+p/2;tv||p)&&(o.rowLastLabelX[e.row]=y,"y"===o.axis?(t.save(),na.labelTransformWithContext(t,c),na.fillText(t,a,c,u,g,h),t.restore()):na.fillText(t,a,c,u,g,h))}finally{t.restore()}}const Id=new Set(["nonsense","missense","stop-loss","frameshift","cds-indel"]),Ed=new Set(["coding-synon"]),Md=new Set(["splice-3","splice-5"]),Rd=new Set(["untranslated-5","untranslated-3"]);function Ld(t,e,i,n,r){var s,o,a,l,h=Cd(t,e,i),c=this.margin,u=this.snpColors.length;switch(s="squished"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case"function":l=t.func.split(",").map((function(t){return Id.has(t)||Md.has(t)?u-1:Ed.has(t)?u-2:Rd.has(t)?u-3:0})),o=l.reduce((function(t,e){return Math.max(t,e)}));break;case"class":o="deletion"===(a=t.class)?u-1:"mnp"===a?u-2:"microsatellite"===a||"named"===a?u-3:0}r.fillStyle=this.snpColors[o],r.fillRect(h.px,c,h.pw,s)}function Bd(t,e,i,n,r){const s="EXPANDED"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let o=this.margin;"COLLAPSED"!==this.displayMode&&void 0!==t.row&&(o+=t.row*s);const a=o+.5*s,l=a-.5*s,h=a+.5*s,c=Math.round((t.junction_left-e)/i),u=Math.round((t.junction_right-e)/i);r.beginPath(),r.moveTo(c,a),r.bezierCurveTo(c,l,u,l,u,a),r.lineWidth=1+Math.log(t.num_junction_reads)/Math.log(2),r.strokeStyle="blue",r.stroke();const d=t.spanning_frag_coords;for(let t=0;te&&(e=i.row);return this.margin+(e+1)*("SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(t){const e=t.features,i=t.context,n=t.bpPerPixel,r=t.bpStart,s=t.pixelWidth,o=t.pixelHeight,a=r+s*n+1;if(this.config.isMergedTrack||na.fillRect(i,0,t.pixelTop,s,o,{fillStyle:"rgb(255, 255, 255)"}),e){const l=[];t.rowLastX=[],t.rowLastLabelX=[];for(let i of e)if(i.start>r&&i.enda)break;const e="COLLAPSED"===this.displayMode?0:s.row;t.drawLabel=t.labelAllFeatures||h>10;const l=Math.ceil((s.end-r)/n),u=c[e];if(!u||l>u){this.render.call(this,s,r,n,o,i,t);const a=Math.floor((s.start-r)/n);u&&a-u<=0&&(i.globalAlpha=.5,na.strokeLine(i,a,0,a,o,{strokeStyle:"rgb(255, 255, 255)"}),i.globalAlpha=1),c[e]=l}}}else console.log("No feature list")}clickedFeatures(t){const e=t.y-this.margin,i=super.clickedFeatures(t);let n;switch(this.displayMode){case"SQUISHED":n=Math.floor(e/this.squishedRowHeight);break;case"EXPANDED":n=Math.floor(e/this.expandedRowHeight);break;default:n=void 0}return i.filter((function(t){return void 0===n||void 0===t.row||n===t.row}))}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=t.genomicLocation,n=[];for(let t of e){const e=t._f||t,r="function"==typeof e.popupData?e.popupData(i):this.extractPopupData(e);if(r){n.length>0&&n.push("

");const s=this.infoURL||this.config.infoURL;for(let e of r)if(n.push(e),s&&e.name&&"name"===e.name.toLowerCase()&&e.value&&ji(e.value)&&!e.value.startsWith("<")){const i=s.replace("$$",t.name);e.value=`${e.value}`}const o="gff"===this.config.format||"gff3"===this.config.format||"gtf"===this.config.format;if(e.exons)for(let t=0;t=r.start&&i<=r.end){const i=o?r.number:"-"===e.strand?e.exons.length-t:t+1;i&&(n.push("
"),n.push({name:"Exon Number",value:i}));break}}}}return n}menuItemList(){const t=[];if(this.render===Ld){t.push("
");for(let e of["function","class"])t.push({object:fe(zi("Color by "+e,e===this.colorBy)),click:()=>{this.colorBy=e,this.trackView.repaintViews()}})}t.push("
");for(let e of["COLLAPSED","SQUISHED","EXPANDED"]){const i={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};t.push({object:fe(zi(i[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.config.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return t}contextMenuItemList(t){const e=this.clickedFeatures(t);if(void 0===e||0===e.length)return;e.length>1&&e.sort(((t,e)=>e.end-e.start-(t.end-t.start)));const i=e[0];if(i.end-i.start<=1e6){const t=[{label:"View feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(i.chr,i.start,i.end);t?"-"===i.strand&&(t=Ra(t)):t="Unknown sequence",this.browser.alert.present(t)}}];return ba()&&void 0!==navigator.clipboard&&t.push({label:"Copy feature sequence",click:async()=>{let t=await this.browser.genome.getSequence(i.chr,i.start,i.end);t?"-"===i.strand&&(t=Ra(t)):t="Unknown sequence";try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}}),t.push("
"),t}}description(){if(Ld===this.render){let t=""+this.name+"
";return t+="Color By Function:
",t+='Red: Coding-Non-Synonymous, Splice Site
',t+='Green: Coding-Synonymous
',t+='Blue: Untranslated
',t+='Black: Intron, Locus, Unknown

',t+="Color By Class:
",t+='Red: Deletion
',t+='Green: MNP
',t+='Blue: Microsatellite, Named
',t+='Black: Indel, Insertion, SNP',t+="",t}return super.description()}getColorForFeature(t){let e;if(this.altColor&&"-"===t.strand)e="function"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)e="function"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const i=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];e=this.colorTable.getColor(i)}else t.color&&(e=t.color);if(e||(e="rgb(0, 0, 150)"),t.alpha&&1!==t.alpha)e=xo.addAlpha(e,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const i=function(t,e,i){const n=(e-t)/9,r=Math.floor((i-t)/n);return Math.min(1,.2+.8*r/9)}(this.config.min?this.config.min:this.viewLimitMin?this.viewLimitMin:0,this.config.max?this.config.max:this.viewLimitMax?this.viewLimitMax:1e3,t.score);t.alpha=i,e=xo.addAlpha(e,i)}return e}dispose(){this.trackView=void 0}}class Fd{constructor(t){this.config=t,this.browser=t.browser,this.columnFormat=t.columnFormat,this.tableRowSelectionList=[],this.tableDOM=_e.div({class:"igv-roi-table"}),t.parent.appendChild(this.tableDOM),this.headerDOM=t,this.tableColumnTitles=this.tableDOM,this.tableRowContainer=this.tableDOM,this.footerDOM=t.gotoButtonHandler}set headerDOM({browser:t,parent:e,headerTitle:i,dismissHandler:n}){const r=_e.div();this.tableDOM.appendChild(r);const s=_e.div();r.appendChild(s),s.innerHTML=i;const o=_e.div();r.appendChild(o),o.appendChild(_i.createIcon("times")),this.boundDismissHandler=function(t){t.stopPropagation(),n()}.bind(this),o.addEventListener("click",this.boundDismissHandler);const{y:a}=t.root.getBoundingClientRect(),{y:l}=e.getBoundingClientRect(),h=-(l-a);Ci(this.tableDOM,r,{minX:0,minY:h}),this.tableDOM.style.display="none",this._headerDOM=r}set tableColumnTitles(t){const e=_e.div({class:"igv-roi-table-column-titles"});t.appendChild(e);for(const{label:t,width:i}of this.columnFormat){const n=_e.div();e.appendChild(n),n.style.width=i,n.innerText=t}this._tableColumnTitlesDOM=e}get tableColumnTitles(){return this._tableColumnTitlesDOM}set tableRowContainer(t){const e=_e.div({class:"igv-roi-table-row-container"});t.appendChild(e),this._tableRowContainerDOM=e}get tableRowContainer(){return this._tableRowContainerDOM}set footerDOM(t){const e=_e.div();this.tableDOM.appendChild(e);const i=_e.div({class:"igv-roi-table-button"});e.appendChild(i),i.id="igv-roi-table-view-button",i.textContent="Go To",i.style.pointerEvents="none",this._footerDOM=e,this.gotoButton=i,this.boundGotoButtonHandler=t.bind(this),this.gotoButton.addEventListener("click",this.boundGotoButtonHandler)}tableRowDOMHelper(t){t.addEventListener("mousedown",(e=>{e.stopPropagation(),t.classList.toggle("igv-roi-table-row-selected"),t.classList.contains("igv-roi-table-row-selected")?t.classList.remove("igv-roi-table-row-hover"):t.classList.add("igv-roi-table-row-hover"),this.setTableRowSelectionState(t.classList.contains("igv-roi-table-row-selected"))})),t.addEventListener("mouseover",(e=>{t.classList.contains("igv-roi-table-row-selected")?t.classList.remove("igv-roi-table-row-hover"):t.classList.add("igv-roi-table-row-hover")})),t.addEventListener("mouseout",(e=>{t.classList.remove("igv-roi-table-row-hover")}))}clearTable(){const t=this.tableRowContainer.querySelectorAll(".igv-roi-table-row");for(let e of t)e.remove()}setTableRowSelectionState(t){t?this.tableRowSelectionList.push(1):this.tableRowSelectionList.pop(),this.gotoButton.style.pointerEvents=this.tableRowSelectionList.length>0?"auto":"none"}present(){this.tableDOM.style.left="0px";const{y:t}=this.browser.root.getBoundingClientRect(),{y:e}=this.config.parent.getBoundingClientRect();this.tableDOM.style.top=t-e+"px",this.tableDOM.style.display="flex"}dismiss(){this.tableDOM.style.display="none"}dispose(){this.tableDOM.innerHTML="",this.tableDOM.remove();for(const t of Object.keys(this))this[t]=void 0;document.removeEventListener("click",this.boundDismissHandler)}}class Od extends Fd{constructor(t){super(Object.assign({width:"1024px"},t)),this.descriptionDOM=t}set descriptionDOM(t){if(t.description){let e;e=_e.div({class:"igv-roi-table-description"}),this.tableDOM.insertBefore(e,this.tableColumnTitles),e.style.height="auto",e.innerHTML="BLAT result for query sequence:",e=_e.div({class:"igv-roi-table-description"}),this.tableDOM.insertBefore(e,this.tableColumnTitles),e.style.height="auto",e.style.maxHeight="128px",e.innerHTML=t.description,e=_e.div({class:"igv-roi-table-goto-explainer"}),this.tableDOM.insertBefore(e,this.tableColumnTitles),e.innerHTML="Select one or more rows and click Go To to view the regions"}}tableRowDOM(t){const e=_e.div({class:"igv-roi-table-row"}),i=t.map((t=>isFinite(t)?$i(t):t));for(let t=0;tt.remove())),t.length>0)for(let e of t){const t=this.tableRowDOM(e);this.tableRowContainer.appendChild(t)}}static getColumnFormatConfiguration(){return[{label:"chr",width:"7%"},{label:"start",width:"12%"},{label:"end",width:"12%"},{label:"strand",width:"5%"},{label:"score",width:"5%"},{label:"match",width:"5%"},{label:"mis-match",width:"7%"},{label:"rep. match",width:"7%"},{label:"N's",width:"3%"},{label:"Q gap count",width:"9%"},{label:"Q gap bases",width:"9%"},{label:"T gap count",width:"9%"},{label:"T gap bases",width:"9%"}]}static gotoButtonHandler(t){t.stopPropagation();const e=this.tableDOM.querySelectorAll(".igv-roi-table-row-selected"),i=[];for(const t of e){const e=[];t.querySelectorAll("div").forEach((t=>e.push(t.innerText)));const[n,r,s]=e;i.push(`${n}:${r}-${s}`)}for(const t of this.tableDOM.querySelectorAll(".igv-roi-table-row"))t.classList.remove("igv-roi-table-row-selected");this.setTableRowSelectionState(!1),this.browser.search(i.join(" "))}}const Dd="https://igv.org/services/blatUCSC.php";async function Pd({url:t,userSeq:e,db:i}){t=t||Dd;const n=await async function(t="",e,i){const n=new URLSearchParams;n.append("userSeq",e),n.append("db",i);return(await fetch(t,{method:"post",body:n})).json()}(t,e,i);return n.fields,n.blat.map(Wl)}const zd=25e3;class Ud extends Nd{constructor(t,e){super(t,e),this.name||(this.name="Blat Results"),this.sequence=t.sequence,this.table=void 0}openTableView(){if(void 0===this.table){const t=this.config.features.map((t=>[t.chr,t.start+1,t.end,t.strand,t.score,t.matches,t.misMatches,t.repMatches,t.nCount,t.qNumInsert,t.qBaseInsert,t.tNumInsert,t.tBaseInsert])),e={browser:this.browser,parent:this.browser.parent,headerTitle:this.config.title,description:this.sequence,dismissHandler:()=>{this.table.dismiss(),this.table.dispose(),this.table=void 0},columnFormat:Od.getColumnFormatConfiguration(),gotoButtonHandler:Od.gotoButtonHandler};this.table=new Od(e),this.table.renderTable(t)}this.table.present()}menuItemList(){const t=super.menuItemList();return t.push("
"),t.push({label:"Open table view",click:()=>this.openTableView()}),t}dispose(){super.dispose(),this.table&&this.table.popover.parentElement.removeChild(this.table.popover)}}async function Vd({sequence:t,browser:e,name:i,title:n}){if(t.length>zd)return void e.alert.present(`Sequence size exceeds maximum allowed length (${t.length} > 25000)`);const r=e.genome.id,s=e.config.blatServerURL;try{const o={type:"blat",name:i||"blat results",title:n||"blat results",sequence:t,altColor:"rgb(176, 176, 236)",color:"rgb(236, 176, 176)",features:await Pd({url:s,userSeq:t,db:r})};(await e.loadTrack(o)).openTableView()}catch(t){e.alert.present(`Error performing blat search: ${t}`)}}const Hd="rgb(185, 185, 185)";class jd extends ch{static defaults={alleleFreqThreshold:.2,visibilityWindow:3e4,showCoverage:!0,showAlignments:!0,viewAsPairs:!1,pairsSupported:!0,showSoftClips:!1,showAllBases:!1,showInsertions:!0,showMismatches:!0,height:300,coverageTrackHeight:50};constructor(t,e){super(t,e)}init(t){this.type="alignment",this.featureSource=new ju(t,this.browser),this.coverageTrack=new $d(t,this),this.alignmentTrack=new qd(t,this),super.init(t),this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.showAlignments||(this._height=this.coverageTrackHeight),t.sort&&(Array.isArray(t.sort)?this.assignSort(t.sort[0]):this.assignSort(t.sort))}set height(t){this._height=t,this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?t-this.coverageTrackHeight:t)}get height(){return this._height}get minTemplateLength(){const t=void 0!==this.config.minTLEN?this.config.minTLEN:this.config.minFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.minTLEN:0}get maxTemplateLength(){const t=void 0!==this.config.maxTLEN?this.config.maxTLEN:this.config.maxFragmentLength;return void 0!==t?t:this._pairedEndStats?this._pairedEndStats.maxTLEN:1e3}sort(t){t=this.assignSort(t);for(let e of this.trackView.viewports)if(e.containsPosition(t.chr,t.position)){const i=e.cachedFeatures;i&&(i.sortRows(t),e.repaint())}}assignSort(t){if(t.locus){const e=function(t){const e=t.split(":"),i=e[1].split("-"),n={chr:e[0],start:Number.parseInt(i[0].replace(/,/g,""))-1};return i.length>1?n.end=Number.parseInt(i[1].replace(/,/g,"")):n.end=n.start+1,n}(t.locus);t.chr=e.chr,t.position=e.start}else t.position--;return t.direction="ASC"===t.direction||!0===t.direction,t.chr=this.browser.genome.getChromosomeName(t.chr),this.sortObject=t,this.sortObject}async getFeatures(t,e,i,n,r){const s=await this.featureSource.getAlignments(t,e,i);if(s.paired&&!this._pairedEndStats&&!this.config.maxFragmentLength){const t=new xd(s.alignments,this.config);t.totalCount>99&&(this._pairedEndStats=t)}s.alignments=void 0;const o=this.sortObject;return o&&o.chr===t&&o.position>=e&&o.position<=i&&s.sortRows(o),s}computePixelHeight(t){return(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(t):0)}draw(t){na.fillRect(t.context,0,t.pixelTop,t.pixelWidth,t.pixelHeight,{fillStyle:"rgb(255, 255, 255)"}),!0===this.showCoverage&&this.coverageTrackHeight>0?(this.trackView.axisCanvas.style.display="block",this.coverageTrack.draw(t)):this.trackView.axisCanvas.style.display="none",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(t))}paintAxis(t,e,i){this.coverageTrack.paintAxis(t,e,this.coverageTrackHeight)}contextMenuItemList(t){return this.alignmentTrack.contextMenuItemList(t)}popupData(t){return!0===this.showCoverage&&t.y>=this.coverageTrack.top&&t.y=this.coverageTrack.top&&t.y=this.coverageTrack.top&&t.y");const e=fe('
');e.text("Color by:"),t.push({name:void 0,object:e,click:void 0,init:void 0});const i=[{key:"strand",label:"read strand"}];this.alignmentTrack.hasPairs&&(i.push({key:"firstOfPairStrand",label:"first-of-pair strand"}),i.push({key:"pairOrientation",label:"pair orientation"}),i.push({key:"tlen",label:"insert size (TLEN)"}),i.push({key:"unexpectedPair",label:"pair orientation & insert size (TLEN)"}));const n="tag"+(this.alignmentTrack.colorByTag?" ("+this.alignmentTrack.colorByTag+")":"");i.push({key:"tag",label:n});for(let e of i){const i=this.alignmentTrack.colorBy===e.key;t.push(this.colorByCB(e,i))}const r=()=>{if(!this.autoHeight){const t=(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(t)}};t.push("
"),t.push({object:fe(zi("Show Coverage",this.showCoverage)),click:()=>{this.showCoverage=!this.showCoverage,r(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:fe(zi("Show Alignments",this.showAlignments)),click:()=>{this.showAlignments=!this.showAlignments,r(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push("
"),t.push({object:fe(zi("Show all bases",this.showAllBases)),click:()=>{this.showAllBases=!this.showAllBases,this.config.showAllBases=this.showAllBases,this.trackView.repaintViews()}}),t.push("
"),t.push({object:fe(zi("Show mismatches",this.showMismatches)),click:()=>{this.showMismatches=!this.showMismatches,this.config.showMismatches=this.showMismatches,this.trackView.repaintViews()}}),t.push({object:fe(zi("Show insertions",this.showInsertions)),click:()=>{this.showInsertions=!this.showInsertions,this.config.showInsertions=this.showInsertions,this.getCachedAlignmentContainers(),this.trackView.repaintViews()}}),t.push({object:fe(zi("Show soft clips",this.showSoftClips)),click:()=>{this.showSoftClips=!this.showSoftClips,this.config.showSoftClips=this.showSoftClips,this.featureSource.setShowSoftClips(this.showSoftClips);const t=this.getCachedAlignmentContainers();for(let e of t)e.setShowSoftClips(this.showSoftClips);this.trackView.repaintViews()}}),this.pairsSupported&&this.alignmentTrack.hasPairs&&(t.push("
"),t.push({object:fe(zi("View as pairs",this.viewAsPairs)),click:()=>{this.viewAsPairs=!this.viewAsPairs,this.config.viewAsPairs=this.viewAsPairs,this.featureSource.setViewAsPairs(this.viewAsPairs);const t=this.getCachedAlignmentContainers();for(let e of t)e.setViewAsPairs(this.viewAsPairs);this.trackView.repaintViews()}})),this.browser.circularView&&(this.alignmentTrack.hasPairs||this.alignmentTrack.hasSupplemental)&&(t.push("
"),this.alignmentTrack.hasPairs&&t.push({label:"Add discordant pairs to circular view",click:()=>{for(let t of this.trackView.viewports)this.addPairedChordsForViewport(t)}}),this.alignmentTrack.hasSupplemental&&t.push({label:"Add split reads to circular view",click:()=>{for(let t of this.trackView.viewports)this.addSplitChordsForViewport(t)}})),t.push("
");const s=fe('
');return s.text("Display mode:"),t.push({name:void 0,object:s,click:void 0,init:void 0}),t.push({object:fe(zi("expand","EXPANDED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="EXPANDED",this.config.displayMode="EXPANDED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t.push({object:fe(zi("squish","SQUISHED"===this.alignmentTrack.displayMode)),click:()=>{this.alignmentTrack.displayMode="SQUISHED",this.config.displayMode="SQUISHED",this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),t}colorByCB(t,e){return{name:void 0,object:fe(zi(t.label,e)),click:e=>{"tag"!==t.key?t.key===this.alignmentTrack.colorBy?(this.alignmentTrack.colorBy="none",this.config.colorBy="none",this.trackView.repaintViews()):(this.alignmentTrack.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews()):this.browser.inputDialog.present({label:"Tag Name",value:this.alignmentTrack.colorByTag?this.alignmentTrack.colorByTag:"",callback:t=>{t?(this.alignmentTrack.colorBy="tag",this.alignmentTrack.colorByTag=t,this.alignmentTrack.tagColors||(this.alignmentTrack.tagColors=new ta("Set1"))):(this.alignmentTrack.colorBy="none",this.alignmentTrack.colorByTag=""),this.trackView.repaintViews()}},e)},init:void 0}}getState(){const t=super.getState();return this.sortObject&&(t.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?"ASC":"DESC"}),t}getCachedAlignmentContainers(){return this.trackView.viewports.map((t=>t.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(t){this.coverageTrack.dataRange=t}get logScale(){return this.coverageTrack.logScale}set logScale(t){this.coverageTrack.logScale=t}get autoscale(){return this.coverageTrack.autoscale}set autoscale(t){this.coverageTrack.autoscale=t}addPairedChordsForViewport(t){const e=this.maxTemplateLength,i=[],n=t.referenceFrame;for(let r of t.cachedFeatures.allAlignments())r.end>=n.start&&r.start<=n.end&&(r.paired?r.end-r.start>e&&i.push(r):r.mate&&r.mate.chr&&(r.mate.chr!==r.chr||Math.max(r.fragmentLength)>e)&&i.push(r));_d((t=>{const e=[];for(let i of t)if(i.paired)i.firstAlignment&&i.secondAlignment&&e.push({uniqueId:i.readName,refName:vd(i.firstAlignment.chr),start:i.firstAlignment.start,end:i.firstAlignment.end,mate:{refName:vd(i.secondAlignment.chr),start:i.secondAlignment.start,end:i.secondAlignment.end}});else{const t=i.mate;t&&t.chr&&t.position&&e.push({uniqueId:i.readName,refName:vd(i.chr),start:i.start,end:i.end,mate:{refName:vd(t.chr),start:t.position-1,end:t.position}})}return e})(i),this,n,.02)}addSplitChordsForViewport(t){const e=[],i=t.referenceFrame;for(let n of t.cachedFeatures.allAlignments()){const t=n.hasTag("SA");n.end>=i.start&&n.start<=i.end&&t&&e.push(n)}_d((t=>{const e=t=>{const e=hu(t.tags().SA);let n=0;for(let r of e)r.start!==t.start&&i.push({uniqueId:`${t.readName}_${n++}`,refName:vd(t.chr),start:t.start,end:t.end,mate:{refName:vd(r.chr),start:r.start,end:r.start+r.lenOnRef}})},i=[];for(let i of t)i.paired?(e(i.firstAlignment),i.secondAlignment&&e(i.secondAlignment)):e(i);return i})(e),this,i,.02)}}class $d{constructor(t,e){this.parent=e,this.featureSource=e.featureSource,this.paintAxis=$u,this.top=0,this.autoscale=t.autoscale||void 0===t.max,this.autoscale||(this.dataRange={min:t.min||0,max:t.max})}get height(){return this.parent.coverageTrackHeight}draw(t){const e=t.pixelTop;t.pixelHeight;const i=this.parent.browser.nucleotideColors;if(e>this.height)return;const n=t.context,r=t.features.coverageMap;let s;r.refSeq&&(s=r.refSeq.toUpperCase());const o=t.bpPerPixel,a=t.bpStart,l=a+t.pixelWidth*o+1;let h;h=this.parent.coverageColor?this.parent.coverageColor:this.parent.color&&"function"!=typeof this.parent.color?xo.darkenLighten(this.parent.color,-35):"rgb(150, 150, 150)",na.setProperties(n,{fillStyle:h,strokeStyle:h});const c=Math.max(1,Math.ceil(1/o));for(let t=0,e=r.coverage.length;tl)break;const i=r.coverage[t];if(!i)continue;const s=Math.round(i.total/this.dataRange.max*this.height),h=this.height-s,u=Math.floor((e-a)/o);na.fillRect(n,u,h,c,s)}if(s)for(let t=0,e=r.coverage.length;tl)break;const h=r.coverage[t];if(!h)continue;const u=h.total/this.dataRange.max*this.height;let d=this.height-u;const f=Math.floor((e-a)/o),p=s[t];if(h.isMismatch(p)){na.setProperties(n,{fillStyle:i[p]}),na.fillRect(n,f,d,c,u);let t=0;for(let e of["A","C","T","G"]){const r=(h["pos"+e]+h["neg"+e])/this.dataRange.max*this.height;d=this.height-r-t,t+=r,na.setProperties(n,{fillStyle:i[e]}),na.fillRect(n,f,d,c,r)}}}}getClickedObject(t){let e=t.viewport.cachedFeatures;if(!e||0===e.length)return;const i=Math.floor(t.genomicLocation),n=e.coverageMap,r=Math.floor(i-n.bpStart);return n.coverage[r]}popupData(t){const e=[],i=this.getClickedObject(t);if(i){const n=Math.floor(t.genomicLocation),r=t.viewport.referenceFrame;e.push(r.chr+":"+$i(1+n)),e.push({name:"Total Count",value:i.total});let s=i.posA+i.negA;s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posA+"+, "+i.negA+"- )"),e.push({name:"A",value:s}),s=i.posC+i.negC,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posC+"+, "+i.negC+"- )"),e.push({name:"C",value:s}),s=i.posG+i.negG,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posG+"+, "+i.negG+"- )"),e.push({name:"G",value:s}),s=i.posT+i.negT,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posT+"+, "+i.negT+"- )"),e.push({name:"T",value:s}),s=i.posN+i.negN,s>0&&(s=s.toString()+" ("+Math.round(s/i.total*100)+"%, "+i.posN+"+, "+i.negN+"- )"),e.push({name:"N",value:s}),e.push("
"),e.push({name:"DEL",value:i.del.toString()}),e.push({name:"INS",value:i.ins.toString()})}return e}}class qd{constructor(t,e){this.parent=e,this.browser=e.browser,this.featureSource=e.featureSource,this.top=0===t.coverageTrackHeight?0:t.coverageTrackHeight+5,this.displayMode=t.displayMode||"EXPANDED",this.alignmentRowHeight=t.alignmentRowHeight||14,this.squishedRowHeight=t.squishedRowHeight||3,this.negStrandColor=t.negStrandColor||"rgba(150, 150, 230, 0.75)",this.posStrandColor=t.posStrandColor||"rgba(230, 150, 150, 0.75)",this.insertionColor=t.insertionColor||"rgb(138, 94, 161)",this.insertionTextColor=t.insertionTextColor||"white",this.showInsertionText=void 0!==t.showInsertionText&&!!t.showInsertionText,this.deletionColor=t.deletionColor||"black",this.deletionTextColor=t.deletionTextColor||"black",this.showDeletionText=void 0!==t.showDeletionText&&!!t.showDeletionText,this.skippedColor=t.skippedColor||"rgb(150, 170, 170)",this.pairConnectorColor=t.pairConnectorColor,this.smallTLENColor=t.smallTLENColor||t.smallFragmentLengthColor||"rgb(0, 0, 150)",this.largeTLENColor=t.largeTLENColor||t.largeFragmentLengthColor||"rgb(200, 0, 0)",this.pairOrientation=t.pairOrienation||"fr",this.pairColors={},this.pairColors.RL=t.rlColor||"rgb(0, 150, 0)",this.pairColors.RR=t.rrColor||"rgb(20, 50, 200)",this.pairColors.LL=t.llColor||"rgb(0, 150, 150)",this.colorBy=t.colorBy||"unexpectedPair",this.colorByTag=t.colorByTag?t.colorByTag.toUpperCase():void 0,this.bamColorTag=void 0===t.bamColorTag?"YC":t.bamColorTag,this.hideSmallIndels=t.hideSmallIndels,this.indelSizeThreshold=t.indelSizeThreshold||1,this.hasPairs=!1,this.hasSupplemental=!1}setTop(t,e){this.top=0===t.height||!1===e?0:5+t.height}computePixelHeight(t){return t.packedAlignmentRows?(t.hasDownsampledIntervals()?10:0)+("SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight)*t.packedAlignmentRows.length+5:0}draw(t){const e=t.features,i=t.context,n=t.bpPerPixel,r=t.bpStart,s=t.pixelWidth,o=r+s*n+1,a=this.parent.showSoftClips,l=this.parent.showAllBases,h=this.browser.nucleotideColors,c=e.packedAlignmentRows;i.save();let u=e.sequence;u&&(u=u.toUpperCase());let d=0,f=t.pixelTop;this.top&&i.translate(0,this.top);const p=f+t.pixelHeight;e.hasDownsampledIntervals()?(d=10,e.downsampledIntervals.forEach((function(t){var e=(t.start-r)/n,s=(t.end-r)/n;s-e>5&&(e+=1,s-=1),na.fillRect(i,e,2,s-e,3,{fillStyle:"black"})}))):d=0,this.alignmentsYOffset=d;const g="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;if(c){const t=c.length;for(let e=0;ep)break;if(!(i+no)break;!0!==e.hidden&&(e instanceof Xc?(m.call(this,e,i,n),b.call(this,e.firstAlignment,i,n),e.secondAlignment&&b.call(this,e.secondAlignment,i,n)):b.call(this,e,i,n))}}}function m(t,e,s){var a=this.getConnectorColor(t.firstAlignment),l=(t.connectingStart-r)/n,h=(t.connectingEnd-r)/n,c=e+s/2;t.connectingEndo||(t.mq<=0&&(a=xo.addAlpha(a,.15)),na.setProperties(i,{fillStyle:a,strokeStyle:a}),na.strokeLine(i,l,c,h,c))}function b(t,c,d){if(t.start+t.lengthOnRefo)return;const f=a?t.blocks:t.blocks.filter((t=>"S"!==t.type));let p=this.getAlignmentColor(t);const m=p;t.mq<=0&&(p=xo.addAlpha(p,.15)),na.setProperties(i,{fillStyle:p,strokeStyle:m});const b=[];for(let t=0;to))break}if(t.gaps){const e=c+d/2;for(let s of t.gaps){const t=(s.start-r)/n,o=(s.start+s.len-r)/n,a=o-t,l=s.len.toString(),h=6*l.length,u=t+a/2,d="D"===s.type?this.deletionColor:this.skippedColor;if(na.strokeLine(i,t,e,o,e,{strokeStyle:d,lineWidth:2}),this.showDeletionText&&s.len>1&&a>=h+8){const t=u-h/2;na.fillRect(i,t-1,c-1,h+2,12,{fillStyle:"white"}),na.fillText(i,l,t,c+10,{font:"normal 10px monospace",fillStyle:this.deletionTextColor})}}}if(t.insertions&&this.parent.showInsertions){let e=-1;for(let s of t.insertions){if(this.hideSmallIndels&&s.len<=this.indelSizeThreshold)continue;if(s.starto)break;const t=s.start-r,a=s.len.toString(),l=2+6*a.length,h=this.showInsertionText&&1!==s.len?Math.round(s.len/n):2,u=Math.max(Math.min(l,h),2),f=t/n-u/2;if(f-e>2){const t={fillStyle:this.insertionColor};na.fillRect(i,f-2,c,u+4,2,t),na.fillRect(i,f,c+2,u,d-4,t),na.fillRect(i,f-2,c+d-2,u+4,2,t),this.showInsertionText&&s.len>1&&h>l&&na.fillText(i,a,f+1,c+10,{font:"normal 10px monospace",fillStyle:this.insertionTextColor}),e=f}}}function y(o,a){const b=[],y=o.start-e.start,v=(o.start-r)/n,w=(o.start+o.len-r)/n,_=Math.max(1,w-v),x=100/n,k=Math.min(g/2,x/6),S="S"===o.type,C=t.mq<=0||this.highlightedAlignmentReadNamed===t.readName||S;let A=m;this.highlightedAlignmentReadNamed===t.readName?A="red":S&&(A="rgb(50,50,50)");const T=!0===t.strand&&a===f.length-1,I=!1===t.strand&&0===a;if(T|I){let t,e;T?(t=[v,w,w+k,w,v,v],e=[c,c,c+d/2,c+d,c+d,c]):I&&(t=[w,v,v-k,v,w,w],e=[c,c,c+d/2,c+d,c+d,c]),na.fillPolygon(i,t,e,{fillStyle:p}),C&&na.strokePolygon(i,t,e,{strokeStyle:A})}else na.fillRect(i,v,c,_,d,{fillStyle:p}),C&&(i.save(),i.strokeStyle=A,i.strokeRect(v,c,_,d),i.restore());if(S||l||this.parent.showMismatches&&u&&t.seq&&"*"!==t.seq){const e=t.seq?t.seq.toUpperCase():void 0,i=t.qual,a=o.seqOffset,f=Math.max(1,1/n);for(let t=0,p=o.len;ts)break;let g=e?e.charAt(a+t):"";const m=y+t>=0?u.charAt(y+t):"";if("="===g&&(g=m),"X"===g||m!==g||S||l){let e;e=!S&&void 0!==i&&i.length>a+t?Wd(i[a+t],h[g]):h[g],e&&b.push({bbox:{x:p,y:c,width:f,height:d},baseColor:e,readChar:g})}}}return b}b.forEach((({bbox:t,baseColor:e,readChar:r})=>{!function(t,e,i,n,r){var s;if(e<=.1&&i.height>=8){const e=Math.min(10,i.height);t.font=e+"px sans-serif",s=i.x+i.width/2,na.strokeText(t,r,s-t.measureText(r).width/2,e-1+i.y,{strokeStyle:n})}else na.fillRect(t,i.x,i.y,i.width,i.height,{fillStyle:n})}(i,n,t,e,r)}))}i.restore()}popupData(t){const e=this.getClickedObject(t);return e?e.popupData(t.genomicLocation):void 0}contextMenuItemList(t){const e=t.viewport,i=[],n=i=>{const n=this.parent.sortObject,r=!n||n.position!==Math.floor(t.genomicLocation)||!n.direction,s={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:i,direction:r};this.parent.sortObject=s,e.cachedFeatures.sortRows(s),e.repaint()};i.push("Sort by..."),i.push({label:"  base",click:()=>n("BASE")}),i.push({label:"  read strand",click:()=>n("STRAND")}),i.push({label:"  insert size",click:()=>n("INSERT_SIZE")}),i.push({label:"  gap size",click:()=>n("GAP_SIZE")}),i.push({label:"  chromosome of mate",click:()=>n("MATE_CHR")}),i.push({label:"  mapping quality",click:()=>n("MQ")}),i.push({label:"  read name",click:()=>n("READ_NAME")}),i.push({label:"  aligned read length",click:()=>n("ALIGNED_READ_LENGTH")}),i.push({label:"  tag",click:()=>{const i=this.parent.sortObject,n=!i||i.position!==Math.floor(t.genomicLocation)||!i.direction,r={label:"Tag Name",value:this.sortByTag?this.sortByTag:"",callback:i=>{if(i){const r={chr:e.referenceFrame.chr,position:Math.floor(t.genomicLocation),option:"TAG",tag:i,direction:n};this.sortByTag=i,this.parent.sortObject=r,e.cachedFeatures.sortRows(r),e.repaint()}}};this.browser.inputDialog.present(r,t.event)}}),i.push("
");const r=this.getClickedObject(t);if(r){const e=this.parent.showSoftClips,n="function"==typeof r.alignmentContaining?r.alignmentContaining(t.genomicLocation,e):r;if(n){n.isPaired()&&n.isMateMapped()&&i.push({label:"View mate in split screen",click:()=>{if(n.mate){const e=t.viewport.referenceFrame;if(this.browser.genome.getChromosome(n.mate.chr)){this.highlightedAlignmentReadNamed=n.readName;const t=e.end-e.start,i=n.mate.position-t/2,r=n.mate.position+t/2;this.browser.addMultiLocusPanel(n.mate.chr,i,r,e)}else this.browser.alert.present(`Reference does not contain chromosome: ${n.mate.chr}`)}},init:void 0}),i.push({label:"View read sequence",click:()=>{const t=n.seq;t&&"*"!==t?this.browser.alert.present(t):this.browser.alert.present("Read sequence: *")}}),ba()&&i.push({label:"Copy read sequence",click:async()=>{const t=n.seq;try{await navigator.clipboard.writeText(t)}catch(t){console.error(t),this.browser.alert.present(`error copying sequence to clipboard ${t}`)}}});const e=n.seq;if(e&&"*"!=e){e.length{const t=n.isNegativeStrand()?Ra(e):e,i=`${n.readName} - blat`,r=`${this.parent.name} - ${i}`;Vd({sequence:t,browser:this.browser,name:i,title:r})}});const t=n.softClippedBlocks();t.left&&t.left.len>20&&t.left.len{const i=e.substr(t.left.seqOffset,t.left.len),r=n.isNegativeStrand()?Ra(i):i,s=`${n.readName} - blat left clip`,o=`${this.parent.name} - ${s}`;Vd({sequence:r,browser:this.browser,name:s,title:o})}}),t.right&&t.right.len>20&&t.right.len{const i=e.substr(t.right.seqOffset,t.right.len),r=n.isNegativeStrand()?Ra(i):i,s=`${n.readName} - blat right clip`,o=`${this.parent.name} - ${s}`;Vd({sequence:r,browser:this.browser,name:s,title:o})}})}i.push("
")}}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&i.push({label:"Add discordant pairs to circular view",click:()=>{this.parent.addPairedChordsForViewport(e)}}),this.hasSupplemental&&i.push({label:"Add split reads to circular view",click:()=>{this.parent.addSplitChordsForViewport(e)}}),i.push("
")),i}getClickedObject(t){const e=t.viewport,i=t.y,n=t.genomicLocation,r=this.parent.showSoftClips;let s=e.cachedFeatures;if(!s||0===s.length)return;let o=s.packedAlignmentRows,a=s.downsampledIntervals;const l="SQUISHED"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let h=Math.floor((i-this.top-this.alignmentsYOffset)/l);if(h<0){for(let t=0;t=n)return a[t]}else if(ht.containsLocation(n,r)));if(t.length>0)return t[0]}}getConnectorColor(t){if(this.pairConnectorColor)return this.pairConnectorColor;switch(this.colorBy){case"strand":case"firstOfPairStrand":case"pairOrientation":case"tag":return this.parent.color?"function"==typeof this.parent.color?this.parent.color(t):this.parent.color:"rgb(200, 200, 200)";default:return this.getAlignmentColor(t)}}getAlignmentColor(t){let e=Hd;e=this.parent.color?"function"==typeof this.parent.color?this.parent.color(t):this.parent.color:Hd;const i=this.colorBy;switch(i){case"strand":e=t.strand?this.posStrandColor:this.negStrandColor;break;case"firstOfPairStrand":t instanceof Xc?e=t.firstOfPairStrand()?this.posStrandColor:this.negStrandColor:t.isPaired()&&(t.isFirstOfPair()?e=t.strand?this.posStrandColor:this.negStrandColor:t.isSecondOfPair()?e=t.strand?this.negStrandColor:this.posStrandColor:console.error("ERROR. Paired alignments are either first or second."));break;case"unexpectedPair":case"pairOrientation":if(this.pairOrientation&&t.pairOrientation){const i=Gd[this.pairOrientation];if(i){const n=this.pairColors[i[t.pairOrientation]];if(n){e=n;break}}}if("pairOrientation"===i)break;case"tlen":case"fragmentLength":t.mate&&t.isMateMapped()&&(t.mate.chr!==t.chr?e=Zd(t.mate.chr):this.parent.minTemplateLength&&Math.abs(t.fragmentLength)this.parent.maxTemplateLength&&(e=this.largeTLENColor));break;case"tag":const n=t.tags()[this.colorByTag];void 0!==n&&(this.bamColorTag===this.colorByTag?e="rgb("+n+")":(this.tagColors||(this.tagColors=new ta("Set1")),e=this.tagColors.getColor(n)))}return e}}function Wd(t,e){let i;return i=t<5?.1:Math.max(.1,Math.min(1,.1+.9*(t-5)/15)),i=Math.round(10*i)/10,i<1&&(e=xo.addAlpha(e,i)),e}const Gd={fr:{F1R2:"LR",F2R1:"LR",F1F2:"LL",F2F1:"LL",R1R2:"RR",R2R1:"RR",R1F2:"RL",R2F1:"RL"},rf:{R1F2:"LR",R2F1:"LR",R1R2:"LL",R2R1:"LL",F1F2:"RR",F2F1:"RR",F1R2:"RL",F2R1:"RL"},ff:{F2F1:"LR",R1R2:"LR",F2R1:"LL",R1F2:"LL",R2F1:"RR",F1R2:"RR",R2R1:"RL",F1F2:"RL"}};function Zd(t){if(Yd[t])return Yd[t];if(Yd["chr"+t]){const e=Yd["chr"+t];return Yd[t]=e,e}{const e=xo.randomRGB(0,255);return Yd[t]=e,e}}const Yd={chrX:"rgb(204, 153, 0)",chrY:"rgb(153, 204, 0)",chrUn:"rgb(50, 50, 50)",chr1:"rgb(80, 80, 255)",chrI:"rgb(139, 155, 187)",chr2:"rgb(206, 61, 50)",chrII:"rgb(206, 61, 50)",chr2a:"rgb(216, 71, 60)",chr2b:"rgb(226, 81, 70)",chr3:"rgb(116, 155, 88)",chrIII:"rgb(116, 155, 88)",chr4:"rgb(240, 230, 133)",chrIV:"rgb(240, 230, 133)",chr5:"rgb(70, 105, 131)",chr6:"rgb(186, 99, 56)",chr7:"rgb(93, 177, 221)",chr8:"rgb(128, 34, 104)",chr9:"rgb(107, 215, 107)",chr10:"rgb(213, 149, 167)",chr11:"rgb(146, 72, 34)",chr12:"rgb(131, 123, 141)",chr13:"rgb(199, 81, 39)",chr14:"rgb(213, 143, 92)",chr15:"rgb(122, 101, 165)",chr16:"rgb(228, 175, 105)",chr17:"rgb(59, 27, 83)",chr18:"rgb(205, 222, 183)",chr19:"rgb(97, 42, 121)",chr20:"rgb(174, 31, 99)",chr21:"rgb(231, 199, 111)",chr22:"rgb(90, 101, 94)",chr23:"rgb(204, 153, 0)",chr24:"rgb(153, 204, 0)",chr25:"rgb(51, 204, 0)",chr26:"rgb(0, 204, 51)",chr27:"rgb(0, 204, 153)",chr28:"rgb(0, 153, 204)",chr29:"rgb(10, 71, 255)",chr30:"rgb(71, 117, 255)",chr31:"rgb(255, 194, 10)",chr32:"rgb(255, 209, 71)",chr33:"rgb(153, 0, 51)",chr34:"rgb(153, 26, 0)",chr35:"rgb(153, 102, 0)",chr36:"rgb(128, 153, 0)",chr37:"rgb(51, 153, 0)",chr38:"rgb(0, 153, 26)",chr39:"rgb(0, 153, 102)",chr40:"rgb(0, 128, 153)",chr41:"rgb(0, 51, 153)",chr42:"rgb(26, 0, 153)",chr43:"rgb(102, 0, 153)",chr44:"rgb(153, 0, 128)",chr45:"rgb(214, 0, 71)",chr46:"rgb(255, 20, 99)",chr47:"rgb(0, 214, 143)",chr48:"rgb(20, 255, 177)"};let Qd,Xd;class Kd extends ml{constructor(t,e,i,n){super(t,e,i,n)}get contentDiv(){return this.$viewport.get(0)}initializationHelper(){let t;this.$multiLocusCloseButton=fe("
",{class:"igv-multi-locus-close-button"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(_i.createIcon("times-circle")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=fe("
",{class:"igv-multi-locus-ruler-label"}),this.$viewport.append(this.$rulerLabel),t=document.createElement("div"),this.$rulerLabel.append(fe(t)),this.$rulerLabel.get(0).addEventListener("click",(async t=>{t.stopPropagation(),await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=fe("
",{class:"igv-ruler-tooltip"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=fe("
"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new Qc(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(ul.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(t){this.$multiLocusCloseButton.show(),this.$rulerLabel.show(),this.$rulerLabel.get(0).style.backgroundColor=Zd(this.referenceFrame.chr);const e=this.$rulerLabel.get(0).querySelector("div"),{width:i}=this.$rulerLabel.get(0).getBoundingClientRect();e.innerHTML=`${this.referenceFrame.getMultiLocusLabel(t)}`;const{width:n}=e.getBoundingClientRect();n/i>.5&&(e.innerHTML=`${this.referenceFrame.getMultiLocusLabelBPLengthOnly(t)}`)}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(t){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===t){const t=this.browser.referenceFrameList.indexOf(this.referenceFrame),e=`click${this.namespace}`;this.$viewport.on(e,(e=>{const{x:i}=_e.translateMouseCoordinates(e,this.$viewport.get(0)),n=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(i));let r;const{chr:s}=this.browser.genome.getChromosomeCoordinate(n);if(1===this.browser.referenceFrameList.length)r=s;else{let e=this.browser.referenceFrameList.map((({locusSearchString:t})=>t));e[t]=s,r=e.join(" ")}this.browser.search(r)})),this.$viewport.get(0).style.cursor="pointer"}else this.$viewport.get(0).style.cursor="default"}mouseMove(t){if(!0===this.browser.cursorGuideVisible){if(void 0===Xd?(Xd=this,this.$tooltip.show()):Xd.guid!==this.guid?(Xd.$tooltip&&Xd.$tooltip.hide(),this.$tooltip.show(),Xd=this):this.$tooltip.show(),this.browser.isMultiLocusWholeGenomeView()||ul.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:e}=_e.translateMouseCoordinates(t,this.$viewport.get(0)),{start:i,bpPerPixel:n}=this.referenceFrame,r=Math.round(.5+i+Math.max(0,e)*n);this.$tooltipContent.text($i(r));const{width:s}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:o}=this.$viewport.get(0).getBoundingClientRect();this.$tooltip.css({left:`${yo(e,0,o-s)}px`}),clearTimeout(Qd),Qd=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4)}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class Jd extends ml{constructor(t,e,i,n){super(t,e,i,n)}initializationHelper(){this.canvas=document.createElement("canvas"),this.canvas.className="igv-ideogram-canvas",this.$viewport.append(fe(this.canvas)),this.ideogram_ctx=this.canvas.getContext("2d"),this.addMouseHandlers()}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(t){this.boundClickHandler=function(t){const{xNormalized:e,width:i}=_e.translateMouseCoordinates(t,this.ideogram_ctx.canvas),{bpLength:n}=this.browser.genome.getChromosome(this.referenceFrame.chr),r=this.referenceFrame.bpPerPixel*i/n;let s=e;s-r/2<0&&(s=r/2),s+r/2>1&&(s=1-r/2);const o=Math.round((s-r/2)*n),a=Math.round((s+r/2)*n);this.referenceFrame.start=o,this.referenceFrame.end=a,this.referenceFrame.bpPerPixel=(a-o)/i,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),t.addEventListener("click",this.boundClickHandler)}setWidth(t){this.$viewport.width(t)}drawSVGWithContext(t,e,i,n,r,s,o){t.saveWithTranslationAndClipRect(n,r,s,e,i,o),this.trackView.track.draw({context:t,referenceFrame:this.referenceFrame,pixelWidth:e,pixelHeight:i}),t.restore()}repaint(){this.draw({referenceFrame:this.referenceFrame})}draw({referenceFrame:t}){na.configureHighDPICanvas(this.ideogram_ctx,this.$viewport.width(),this.$viewport.height()),this.trackView.track.draw({context:this.ideogram_ctx,referenceFrame:t,pixelWidth:this.$viewport.width(),pixelHeight:this.$viewport.height()})}startSpinner(){}stopSpinner(){}}function tf(t,e,i,n){return"ruler"===t.track.type?new Kd(t,e,i,n):"ideogram"===t.track.id?new Jd(t,e,i,n):new ml(t,e,i,n)}const ef={textAlign:"start",textBaseline:"bottom",strokeStyle:"black",fillStyle:"black"};class nf{constructor(t,e,i,n){this.guid=_e.guid(),this.trackView=t,this.browser=t.browser,this.viewport=_e.div({class:"igv-viewport"}),e.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement("canvas"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext("2d"),this.trackScrollDelta=0,this.contentTop=0,this.setWidth(n),!1===this.browser.showSampleNames&&this.hide(),this.addMouseHandlers()}checkCanvas(){const t=window.devicePixelRatio,e=this.viewport.clientHeight,i=this.browser.sampleNameViewportWidth;if(this.canvas.width!==i*t||this.canvas.height!==e*t){const n=this.canvas;n.width=i*t,n.height=e*t,n.style.width=`${i}px`,n.style.height=`${e}px`,this.ctx=this.canvas.getContext("2d"),this.ctx.scale(t,t)}}setTop(t){if("function"==typeof this.trackView.track.getSamples){this.contentTop=t;const e=this.trackView.track.getSamples();this.repaint(e)}}setWidth(t){this.viewport.innerWidth=t,this.checkCanvas()}show(){this.viewport.style.display="block"}hide(){this.viewport.style.display="none"}async repaint(t){this.checkCanvas(),this.draw({context:this.ctx,samples:t})}draw({context:t,samples:e}){if(!e||0===e.names.length)return;!function(t,{textAlign:e,textBaseline:i,strokeStyle:n,fillStyle:r},s){const o=Math.min(s,10);t.font=`${o}px sans-serif`,t.textAlign=e,t.textBaseline=i,t.fillStyle=r}(t,ef,e.height),t.clearRect(0,0,t.canvas.width,t.canvas.height),t.fillStyle=function(t){const{r:e,g:i,b:n}=Ko.lead;return`rgb(${e},${i},${n})`}();const i=this.viewport.getBoundingClientRect().height;let n=(e.yOffset||0)+this.contentTop;for(let r of e.names){if(n>i)break;if(n+e.height>0){const i=r,s=rf(t,i,n,e.height);t.fillText(i,4,s)}n+=e.height}}renderSVGContext(t,{deltaX:e,deltaY:i}){if("function"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:s,height:o}=this.viewport.getBoundingClientRect(),a=`${(this.trackView.track.name||this.trackView.track.id).replace(/\W/g,"")}_sample_names_guid_${_e.guid()}`;t.saveWithTranslationAndClipRect(a,e,i+r,s,o,-r),this.draw({context:t,samples:n}),t.restore()}}addMouseHandlers(){this.addViewportContextMenuHandler(this.viewport)}removeMouseHandlers(){this.removeViewportContextMenuHandler(this.viewport)}addViewportContextMenuHandler(t){this.boundContextMenuHandler=function(t){t.preventDefault(),t.stopPropagation();const e={label:"Name Panel Width",value:this.browser.sampleNameViewportWidth,callback:t=>{this.browser.sampleNameViewportWidth=parseInt(t);for(let{sampleNameViewport:t}of this.browser.trackViews)t.setWidth(this.browser.sampleNameViewportWidth);this.browser.layoutChange()}};this.browser.inputDialog.present(e,t)}.bind(this),t.addEventListener("contextmenu",this.boundContextMenuHandler)}removeViewportContextMenuHandler(t){t.removeEventListener("contextmenu",this.boundContextMenuHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function rf(t,e,i,n){return i+n-function(t,e,i){const{actualBoundingBoxAscent:n,actualBoundingBoxDescent:r}=t.measureText(e);return(i-(n+r))/2}(t,e,n)}const sf=function(t){this.popover=_e.div({class:"igv-menu-popup"}),t.appendChild(this.popover);const e=_e.div({class:"igv-menu-popup-header"});this.popover.appendChild(e),ki.attachDialogCloseHandlerWithParent(e,(()=>this.hide())),this.popoverContent=_e.div(),this.popover.appendChild(this.popoverContent),Ci(this.popover,e),e.addEventListener("click",(t=>{t.stopPropagation(),t.preventDefault()})),this.hide()};sf.prototype.hide=function(){this.popover.style.display="none"},sf.prototype.presentMenuList=function(t){if(of(),t.length>0){this.popoverContent.innerHTML="",t=Ui.trackMenuItemListHelper(t,this);for(let e of t){e.init&&e.init();let i=e.object;0===t.indexOf(e)&&i.removeClass("igv-track-menu-border-top"),i.hasClass("igv-track-menu-border-top")||i.hasClass("igv-menu-popup-check-container")||i.is("div")&&i.addClass("igv-menu-popup-shim"),this.popoverContent.appendChild(i.get(0))}this.popover.style.display="flex";const{width:e}=this.popover.getBoundingClientRect();this.popover.style.left=-e+"px",this.popover.style.top="0px"}},sf.prototype.presentTrackContextMenu=function(t,e){this.popoverContent.innerHTML="";const i=(n=e,r=this.popover,n.map((t=>{let e;if("string"==typeof t&&"
"===t)e=document.createElement("hr");else if("string"==typeof t)e=_e.div({class:"context-menu"}),e.innerHTML=t;else if("Node"==typeof t)e=t;else{if("function"==typeof t.init&&t.init(),"checkbox"===t.type)e=zi("Show all bases",t.value);else if("color"===t.type){const i=new Pi({parent:r.parentElement,width:364});i.configure(void 0,{color:e=>t.click(e)}),e=_e.div({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);const n=t=>{i.show(),_e.hide(r),t.preventDefault(),t.stopPropagation()};e.addEventListener("click",n),e.addEventListener("touchend",n),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}else e=_e.div({class:"context-menu"}),"string"==typeof t.label&&(e.innerHTML=t.label);if(t.click&&"color"!==t.type){function s(e){t.click(),_e.hide(r),e.preventDefault(),e.stopPropagation()}e.addEventListener("click",s),e.addEventListener("touchend",s),e.addEventListener("mouseup",(function(t){t.preventDefault(),t.stopPropagation()}))}}return{el:e,init:t.init}})));var n,r;for(let{el:t}of i)this.popoverContent.appendChild(t);!function(t,e){e.style.display="flex";const{x:i,y:n}=_e.translateMouseCoordinates(t,e.parentNode),{width:r}=e.getBoundingClientRect(),s=i+r,{width:o}=e.parentNode.getBoundingClientRect();e.style.left=`${s>o?i-(s-o):i}px`,e.style.top=`${n}px`}(t,this.popover)},sf.prototype.dispose=function(){this.popoverContent.innerHTML="",this.popover.innerHTML="",Object.keys(this).forEach((function(t){this[t]=void 0}))};const of=()=>{const t=document.querySelectorAll(".igv-menu-popup");for(let e=0;e0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(t,e,i){this.axis=this.createAxis(t,this.track),this.viewports=[];const n=t.calculateViewportWidth(i.length),r=e.querySelectorAll(".igv-column");for(let t=0;t{t.dataRangeDialog.configure(this),t.dataRangeDialog.present(fe(t.columnContainer))}));const{width:n,height:r}=i.getBoundingClientRect();this.axisCanvas=document.createElement("canvas"),this.axisCanvas.style.width=`${n}px`,this.axisCanvas.style.height=`${r}px`,i.appendChild(this.axisCanvas)}return i}resizeAxisCanvas(t,e){this.axis.style.width=`${t}px`,this.axis.style.height=`${e}px`,"function"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${t}px`,this.axisCanvas.style.height=`${e}px`)}removeDOMFromColumnContainer(){this.boundAxisClickHander&&this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.$viewport.remove();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}renderSVGContext(t,{deltaX:e,deltaY:i}){!function(t,e,i,n,r){if("function"==typeof e.paintAxis){const{y:s,width:o,height:a}=i.getBoundingClientRect(),l=`${(e.name||e.id).replace(/\W/g,"")}_axis_guid_${_e.guid()}`;t.saveWithTranslationAndClipRect(l,n,s+r,o,a,0),e.paintAxis(t,o,a),t.restore()}}(t,this.track,this.axisCanvas,e,i);const{width:n}=this.axis.getBoundingClientRect(),{y:r}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let s={deltaX:n+e,deltaY:r+i};for(let e of this.viewports){e.renderSVGContext(t,s);const{width:i}=e.$viewport.get(0).getBoundingClientRect();s.deltaX+=i}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(t,s)}dataRange(){return this.track.dataRange?this.track.dataRange:void 0}setDataRange(t,e){void 0!==t&&(this.track.dataRange.min=t),void 0!==e&&(this.track.dataRange.max=e),this.track.autoscale=!1,this.repaintViews()}presentColorPicker(t){if(!1===lf.has(this.track.type)){const e=[],i=this.track.color||this.track.defaultColor;ji(i)&&e.push(i),this.track.altColor&&ji(this.track.altColor)&&e.push(this.track.altColor);const n=e.map((t=>t.startsWith("#")?t:t.startsWith("rgb(")?xo.rgbToHex(t):xo.colorNameToHex(t))),r={color:t=>{this.track.color=t,this.repaintViews()},altColor:t=>{this.track.altColor=t,this.repaintViews()}};this.browser.genericColorPicker.configure(n,r),this.browser.genericColorPicker.setActiveColorHandler(t),this.browser.genericColorPicker.show()}}setTrackHeight(t,e){e||(this.track.minHeight&&(t=Math.max(this.track.minHeight,t)),this.track.maxHeight&&(t=Math.min(this.track.maxHeight,t))),this.track.height=t,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),"function"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:e}of this.viewports)e.height(t);if(this.sampleNameViewport.viewport.style.height=`${t}px`,"function"!=typeof this.track.computePixelHeight)for(let e of this.viewports)e.setContentHeight(t);this.repaintViews(),!1===af.has(this.track.type)&&this.updateScrollbar(),this.dragHandle.style.height=`${t}px`,this.gearContainer.style.height=`${t}px`}updateScrollbar(){const t=this.viewports[0].$viewport.height();this.outerScroll.style.height=`${t}px`;const e=this.maxViewportContentHeight(),i=Math.round(t/e*t);e>t?(this.innerScroll.style.display="block",this.innerScroll.style.height=`${i}px`):this.innerScroll.style.display="none"}moveScroller(t){const e=fe(this.innerScroll).position().top+t,i=Math.min(Math.max(0,e),this.outerScroll.clientHeight-this.innerScroll.clientHeight);fe(this.innerScroll).css("top",`${i}px`);const n=this.maxViewportContentHeight(),r=-Math.round(i*(n/this.viewports[0].$viewport.height()));for(let t of this.viewports)t.setTop(r);this.sampleNameViewport.trackScrollDelta=t,this.sampleNameViewport.setTop(r)}isLoading(){for(let t of this.viewports)if(t.isLoading())return!0}repaintViews(){for(let t of this.viewports)t.isVisible()&&t.repaint();"function"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSamples()}repaintSamples(){if("function"==typeof this.track.getSamples){const t=this.track.getSamples();this.sampleNameViewport.repaint(t)}}setTrackLabelName(t){this.viewports.forEach((e=>e.setTrackLabel(t)))}resize(t){for(let e of this.viewports)e.setWidth(t)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const t=this.viewports.filter((t=>t.isVisible()));if(t.forEach((t=>t.shift())),this.browser.dragObject)return;const e=t.filter((t=>t.needsRepaint())).filter((t=>t.checkZoomIn())),i=e.filter((t=>t.needsReload()));for(let t of i)await t.loadFeatures();if(this.disposed)return;if(this.track&&"function"==typeof this.track.variantRowCount&&i.length>0){let t=0;for(let e of this.viewports)e.featureCache&&e.featureCache.features&&(t=Math.max(t,e.featureCache.features.reduce(((t,e)=>Math.max(t,e.row||0)),0)));if(this.track.nVariantRows!==t+1){this.track.variantRowCount(t+1);for(let t of this.viewports)t.checkContentHeight()}}if(this.track.autoscale){let e=[];for(let i of t){const t=i.referenceFrame,n=t.start,r=n+t.toBP(i.getWidth());if(i.featureCache&&i.featureCache.features)if("function"==typeof i.featureCache.features.getMax){const t=i.featureCache.features.getMax(n,r);e.push({value:t})}else{const t=Xo(i.featureCache.features,n,r);for(let i of t)e.push(i)}}"function"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(e):this.track.dataRange=ha(e)}const n=this.track.autoscale||this.track.autoscaleGroup||"ruler"===this.track.type;for(let i of t)e.includes(i)?i.repaint():n&&i.refresh();this.adjustTrackHeight(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let t of this.viewports)t.clearCache()}updateRulerViewportLabels(){const t=this.browser.calculateViewportWidth(this.viewports.length);for(let e of this.viewports)"ruler"===this.track.type&&(this.viewports.length>1?e.presentLocusLabel(t):e.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let t=[];const e=this.viewports.filter((t=>t.isVisible()));for(let i of e){const e=i.referenceFrame,{chr:n,start:r,bpPerPixel:s}=i.referenceFrame,o=r+e.toBP(i.getWidth());if((!i.featureCache||!i.featureCache.containsRange(n,r,o,s))&&await i.loadFeatures(),i.featureCache&&i.featureCache.features)if("function"==typeof i.featureCache.features.getMax){const e=i.featureCache.features.getMax(r,o);t.push({value:e})}else{const e="function"==typeof i.featureCache.queryFeatures?i.featureCache.queryFeatures(n,r,o):Xo(i.featureCache.features,r,o);t=t.concat(e)}}return t}checkContentHeight(){for(let t of this.viewports)t.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var t=this.maxViewportContentHeight();if(this.track.autoHeight?this.setTrackHeight(t,!1):this.track.paintAxis&&this.paintAxis(),!1===af.has(this.track.type)){const e=this.viewports[0].getContentTop(),i=this.viewports[0].$viewport.height(),n=Math.min(0,i-t);if(e{t.preventDefault(),void 0===e&&t.target.classList.remove("igv-track-drag-handle-hover")})),this.boundTrackDragMouseOutHandler=s.bind(this),this.dragHandle.addEventListener("mouseout",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){"ideogram"===this.track.id||"ruler"===this.track.id||(this.dragHandle.removeEventListener("mousedown",this.boundTrackDragMouseDownHandler),document.removeEventListener("mouseup",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener("mouseup",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener("mouseout",this.boundTrackDragMouseOutHandler))}addTrackGearMouseHandlers(){if(!0===this.track.ignoreTrackMenu);else{function t(t){t.preventDefault(),t.stopPropagation(),this.trackGearPopup.presentMenuList(Ui.trackMenuItemList(this))}this.boundTrackGearClickHandler=t.bind(this),this.gear.addEventListener("click",this.boundTrackGearClickHandler)}}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener("click",this.boundTrackGearClickHandler)}dispose(){this.removeAxisEventListener(this.axis),this.axis.remove();for(let t of this.viewports)t.dispose();this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),"function"==typeof this.track.dispose&&this.track.dispose();for(let t of Object.keys(this))this[t]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if("function"==typeof this.track.paintAxis){const{width:t,height:e}=this.axisCanvas.getBoundingClientRect(),i=window.devicePixelRatio||1;this.axisCanvas.height=i*e,this.axisCanvas.width=i*t;const n=this.axisCanvas.getContext("2d");n.scale(i,i),this.track.paintAxis(n,t,e)}}maxViewportContentHeight(){return Math.max(this.viewports.map((t=>t.getContentHeight())))}}const cf="rgb(150, 150, 150)";class uf extends ch{static defaults={height:50,flipAxis:!1,logScale:!1,windowFunction:"mean",graphType:"bar",autoscale:!0,normalize:void 0,scaleFactor:void 0};constructor(t,e){super(t,e)}init(t){super.init(t),this.type="wig",this.featureType="numeric",this.paintAxis=$u;const e=t.format?t.format.toLowerCase():t.format;t.featureSource?(this.featureSource=t.featureSource,delete t.featureSource):this.featureSource="bigwig"===e?new Lc(t,this.browser.genome):"tdf"===e?new Dc(t,this.browser.genome):$c(t,this.browser.genome),void 0===t.max||!0===t.autoscale?this.autoscale=!0:this.dataRange={min:t.min||0,max:t.max}}async postInit(){const t=await this.getHeader();this.disposed||t&&this.setTrackProperties(t)}async getFeatures(t,e,i,n){const r=await this.featureSource.getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow,windowFunction:this.windowFunction});if(this.normalize&&this.featureSource.normalizationFactor){const t=this.featureSource.normalizationFactor;for(let e of r)e.value*=t}if(this.scaleFactor){const t=this.scaleFactor;for(let e of r)e.value*=t}return r}menuItemList(){let t=[];return void 0!==this.flipAxis&&(t.push("
"),t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}})),t=t.concat(Ui.numericDataMenuItems(this.trackView)),t}async getHeader(){return"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(t,e,i,n){return n?i/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):i/(e-t)}computeYPixelValue(t,e){return(this.flipAxis?t-this.dataRange.min:this.dataRange.max-t)*e}computeYPixelValueInLogScale(t,e){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),t=Math.log10(t+1),(this.flipAxis?t-n:i-t)*e)}draw(t){const e=t.features,i=t.context,n=t.bpPerPixel,r=t.bpStart,s=t.pixelWidth;t.pixelHeight;const o=r+s*n+1,a=this.color||cf;let l;"string"==typeof a&&a.startsWith("rgb(")&&(l=xo.addAlpha(a,.1));const h=this.getScaleFactor(this.dataRange.min,this.dataRange.max,t.pixelHeight,this.logScale),c=t=>this.logScale?this.computeYPixelValueInLogScale(t,h):this.computeYPixelValue(t,h);if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){let s,a=-1;const h=c(0);for(let t of e){if(t.endo)break;const e=Math.floor((t.start-r)/n);if(isNaN(e))continue;let l=c(t.value);const u=Math.ceil((t.end-r)/n),d=Math.max(1,u-e),f=this.getColorForFeature(t);if("points"===this.graphType){const t=this.config.pointSize||3,n=e+d/2;na.fillCircle(i,n,l,t/2,{fillStyle:f,strokeStyle:f})}else if("line"===this.graphType)null!=s&&na.strokeLine(i,a,s,e,l,{fillStyle:f,strokeStyle:f}),na.strokeLine(i,e,l,e+d,l,{fillStyle:f,strokeStyle:f});else{const t=l-h;na.fillRect(i,e,h,d,t,{fillStyle:f})}a=e+d,s=l}if(this.dataRange.min<0){const e=this.dataRange.max/(this.dataRange.max-this.dataRange.min)*t.pixelHeight;na.strokeLine(i,0,e,t.pixelWidth,e,{strokeStyle:l})}}if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let i=c(e.y),n={strokeStyle:e.color,strokeWidth:2};e.dotted?na.dashedLine(t.context,0,i,t.pixelWidth,i,5,n):na.strokeLine(t.context,0,i,t.pixelWidth,i,n)}}popupData(t,e){if(void 0===e&&(e=this.clickedFeatures(t)),e&&e.length>0){const i=t.genomicLocation,n=[];e.sort((function(t,e){return Math.abs((t.start+t.end)/2-i)-Math.abs((e.start+e.end)/2-i)}));const r=e.length>10?e.slice(0,10):e;r.sort((function(t,e){return t.start-e.start}));for(let t of r)if(t){n.length>0&&n.push("
");let e=t.end-t.start==1?$i(t.start+1):$i(t.start+1)+"-"+$i(t.end);n.push({name:"Position:",value:e}),n.push({name:"Value:     ",value:$i(t.value)})}return r.length..."),n}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}getColorForFeature(t){let e=t.value<0&&this.altColor?this.altColor:this.color||cf;return"function"==typeof e?e(t.value):e}dispose(){this.trackView=void 0}}function df(t){this.thresholds=t.thresholds,this.colors=t.colors}function ff(t){this.scale=t,this.lowColor="rgb("+t.lowR+","+t.lowG+","+t.lowB+")",this.highColor="rgb("+t.highR+","+t.highG+","+t.highB+")",this.diff=t.high-t.low}df.prototype.getColor=function(t){for(let e of this.thresholds)if(t=i.high?this.highColor:(e=(t-i.low)/this.diff,"rgb("+Math.floor(i.lowR+e*(i.highR-i.lowR))+","+Math.floor(i.lowG+e*(i.highG-i.lowG))+","+Math.floor(i.lowB+e*(i.highB-i.lowB))+")")};class pf{constructor(t){this.color=t}getColor(){return this.color}}class gf extends ch{constructor(t,e){super(t,e)}init(t){if(super.init(t),this.type=t.type||"seg","maf"===this.type&&(this.type="mut"),this.isLog=t.isLog,this.displayMode=t.displayMode||"EXPANDED",this.height=t.height||300,this.maxHeight=t.maxHeight||500,this.squishedRowHeight=t.sampleSquishHeight||t.squishedRowHeight||2,this.expandedRowHeight=t.sampleExpandHeight||t.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,t.color?this.color=t.color:(this.posColorScale=t.posColorScale||new ff({low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0}),this.negColorScale=t.negColorScale||new ff({low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255}),"mut"===this.type&&(this.colorTable=new ea(t.colorTable||mf))),this.sampleKeys=[],this.sampleNames=new Map,t.samples){for(let e of t.samples)this.sampleKeys.push(e),this.sampleNames.set(e,e);this.explicitSamples=!0}const e=Object.assign({},this.config);e.maxWGCount=e.maxWGCount||Number.MAX_SAFE_INTEGER,this.featureSource=$c(e,this.browser.genome),this.initialSort=t.sort}async postInit(){"function"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const t=[],e={SQUISHED:"Squish",EXPANDED:"Expand",FILL:"Fill"};t.push("
"),t.push("DisplayMode:");const i="seg"===this.type?["SQUISHED","EXPANDED","FILL"]:["SQUISHED","EXPANDED"];for(let n of i){const i=zi(e[n],n===this.displayMode);t.push({object:fe(i),click:()=>{this.displayMode=n,this.config.displayMode=n,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return t}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys.map((t=>this.sampleNames.get(t))),height:this.sampleHeight,yOffset:0}}async getFeatures(t,e,i){const n=await this.featureSource.getFeatures({chr:t,start:e,end:i});if(this.initialSort){const t=this.initialSort;this.sortSamples(t.chr,t.start,t.end,t.direction,n),this.initialSort=void 0}return n}draw({context:t,renderSVG:e,pixelTop:i,pixelWidth:n,pixelHeight:r,features:s,bpPerPixel:o,bpStart:a}){if(na.fillRect(t,0,i,n,r,{fillStyle:"rgb(255, 255, 255)"}),s&&s.length>0){this.checkForLog(s),this.updateSampleKeys(s);const e={};let l;switch(this.sampleKeys.forEach((function(t,i){e[t]=i})),this.displayMode){case"FILL":this.sampleHeight=r/this.sampleKeys.length,l=0;break;case"SQUISHED":this.sampleHeight=this.squishedRowHeight,l=0;break;default:this.sampleHeight=this.expandedRowHeight,l=1}const h=this.sampleHeight;for(let t of s)t.pixelRect=void 0;const c=i+r,u=a+n*o+1,d=o;this.sampleYStart=void 0;for(let n of s){if(n.endu)break;const r=n.sampleKey||n.sample;n.row=e[r];const s=n.row*h+l;if(void 0===this.sampleYStart&&(this.sampleYStart=s),s+hc)continue;const o=Math.max(n.start,a);let f=Math.round((o-a)/d);const p=Math.min(n.end,u),g=Math.round((p-a)/d);let m,b,y=Math.max(1,g-f);if(this.color?m="function"==typeof this.color?this.color(n):this.color:this.colorTable&&(m=this.colorTable.getColor(n.value.toLowerCase())),"mut"===this.type)b=h-2*l,y<3&&(y=3,f-=1);else{let t=n.value;this.isLog||(t=vo(t/2)),m=t<-.1?this.negColorScale.getColor(t):t>.1?this.posColorScale.getColor(t):"white";let e=h;if(h<.25){const i=.1+2*Math.abs(t);e=Math.min(1,i*h)}b=e-2*l}n.pixelRect={x:f,y:s,w:y,h:b},t.fillStyle=m,t.fillRect(f,s,y,b)}}}checkForLog(t){if(void 0===this.isLog){this.isLog=!1;for(let e of t)if(e.value<0)return void(this.isLog=!0)}}computePixelHeight(t){if(!t)return 0;const e="SQUISHED"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(t),this.sampleKeys.length*e}async sortSamples(t,e,i,n,r){if(r||(r=await this.featureSource.getFeatures({chr:t,start:e,end:i})),!r)return;this.updateSampleKeys(r);const s={},o="ASC"===n?1:-1;"mut"===this.type?(()=>{for(let t of r){if(t.endi)break;const n=t.sampleKey||t.sample;(!s.hasOwnProperty(n)||t.value.localeCompare(s[n])>0)&&(s[n]=t.value)}this.sampleKeys.sort((function(t,e){let i=s[t]||"",n=s[e]||"";return o*i.localeCompare(n)}))})():(()=>{const t=i-e+1;for(let n of r){if(n.endi)break;const r=Math.max(e,n.start),o=(Math.min(i,n.end)-r)/t,a=n.sampleKey||n.sample,l=s[a]||0;s[a]=l+o*n.value}this.sampleKeys.sort((function(t,e){let i=s[t],n=s[e];return i||(i=o*Number.MAX_VALUE),n||(n=o*Number.MAX_VALUE),i===n?0:i>n?o:-1*o}))})(),this.trackView.repaintViews()}clickedFeatures(t){const e=super.clickedFeatures(t),i=t.y;return e.filter((function(t){const e=t.pixelRect;return e&&i>=e.y&&i<=e.y+e.h}))}hoverText(t){const e=this.clickedFeatures(t);if(e&&e.length>0)return`${e[0].sample}: ${e[0].value}`}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=[];for(let t of e){i.length>0&&(i.push("
"),i.push("
"));const e=t._f||t,n="function"==typeof e.popupData?e.popupData(this.type,this.browser.genome.id):this.extractPopupData(e);Array.prototype.push.apply(i,n)}return i}contextMenuItemList(t){const e=t.viewport.referenceFrame,i=t.genomicLocation,n=this.config.sort?"ASC"===this.config.sort.direction?"DESC":"ASC":"DESC",r=e.toBP(2.5),s=e=>{const i=t.viewport.cachedFeatures;this.sortSamples(e.chr,e.start,e.end,e.direction,i)};return[{label:"seg"===this.type?"Sort by value":"Sort by type",click:e=>{const o={direction:n,chr:t.viewport.referenceFrame.chr,start:i-r,end:i+r};s(o),this.config.sort=o}}]}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(t){if(!this.explicitSamples)for(let e of t){const t=e.sampleKey||e.sample;this.sampleNames.has(t)||(this.sampleNames.set(t,e.sample),this.sampleKeys.push(t))}}}const mf={indel:"rgb(0,200,0)","targeted region":"rgb(236,155,43)",truncating:"rgb(\t150,0,0)","non-coding transcript":"rgb(0,0,150)",synonymous:"rgb(109,165,95)",silent:"rgb(109,135,80)",missense_mutation:"rgb(72,130,187)",missense:"rgb(72,130,187)","splice site":"rgb(143,83,155)",splice_region:"rgb(143,83,155)",nonsense:"rgb(216, 57,81)",nonsense_mutation:"rgb(216, 57,81)",frame_shift_del:"rgb(226,135,65)",frame_shift_ins:"rgb(226,135,65)",in_frame_del:"rgb(247,235,94)",in_frame_ins:"rgb(247,235,94)","*other*":"rgb(159,91,50)"};class bf extends ch{constructor(t,e){super(t,e),this.type="merged",this.featureType="numeric",this.paintAxis=$u,this.graphType=t.graphType}init(t){if(!t.tracks)throw Error("Error: no tracks defined for merged track"+t);super.init(t)}async postInit(){this.tracks=[];const t=[];for(let e of this.config.tracks){e.isMergedTrack=!0;const i=await this.browser.createTrack(e);i?(i.autoscale=!1,this.tracks.push(i)):console.warn("Could not create track "+e),"function"==typeof i.postInit&&t.push(i.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale||void 0===this.config.max,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return this.height=this.config.height||50,Promise.all(t)}get height(){return this._height}set height(t){if(this._height=t,this.tracks)for(let e of this.tracks)e.height=t,e.config.height=t}menuItemList(){let t=[];return void 0!==this.flipAxis&&t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),t=t.concat(Ui.numericDataMenuItems(this.trackView)),t}async getFeatures(t,e,i,n){const r=this.tracks.map((r=>r.getFeatures(t,e,i,n))),s=await Promise.all(r);return new yf(s)}draw(t){const e=t.features;for(let i=0,n=this.tracks.length;i0&&i.push("
"),i.push(`
${this.tracks[n].name}
`);const r=this.tracks[n].popupData(t,e[n]);i.push(...r)}return i}}}clickedFeatures(t){const e=t.viewport.cachedFeatures;if(!e)return[];const i=t.genomicLocation,n=[];for(let r of e.featureArrays){const e=t.referenceFrame.bpPerPixel>.2?3*t.referenceFrame.bpPerPixel:.2,s=Xo(r,i-e,i+e);for(let t of s)n.push(t)}return n}get supportsWholeGenome(){return this.tracks.every((t=>t.supportsWholeGenome))}}class yf{constructor(t){this.featureArrays=t}getMax(t,e){let i=-Number.MAX_VALUE;for(let n of this.featureArrays)for(let r of n)if(void 0!==r.value&&!Number.isNaN(r.value)){if(r.ende)break;i=Math.max(i,r.value)}return i}}class vf extends ch{static defaults={height:250,theta:Math.PI/4,arcOrientation:!0,showBlocks:!0,blockHeight:3,thickness:1,alpha:.02,logScale:!0};constructor(t,e){super(t,e)}init(t){super.init(t),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.arcType=function(t){if(!t.arcType)return"nested";switch(t.arcType){case"chiapet":return"inView";case"chiapetoutbound":return"partialInView";default:return t.arcType}}(t),this.alpha=t.alpha||.02,this.painter={flipAxis:!this.arcOrientation,dataRange:this.dataRange,paintAxis:$u},t.valueColumn?(this.valueColumn=t.valueColumn,this.hasValue=!0):t.useScore&&(this.hasValue=!0,this.valueColumn="score"),t.max?(this.dataRange={min:t.min||0,max:t.max},this.autoscale=!1):this.autoscale=!0,t.featureSource?(this.featureSource=t.featureSource,delete t._featureSource):(this.featureSource=$c(t,this.browser.genome),this.featureSource.getWGFeatures=Sf)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,i){const n=this.visibilityWindow,r=await this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:n});return void 0===this.hasValue&&r&&r.length>0&&(this.hasValue=void 0!==r[0].score),r}draw(t){"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?this.drawProportional(t):this.drawNested(t)}drawNested(t){const e=t.context,i=t.pixelWidth,n=t.pixelHeight,r=t.viewportWidth,s=t.bpPerPixel,o=t.bpStart,a=s;na.fillRect(e,0,t.pixelTop,i,n,{fillStyle:"rgb(255, 255, 255)"});const l=t.features;if(l){(function(){let t=0;for(let e of l){let n=(e.start-o)/a,r=(e.end-o)/a;n>=0&&r<=i&&(t=Math.max(t,r-n))}let e=Math.min(r,t)/2;if(t>0){let t=(n-10)/e;this.theta=function(t){let e,i=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],n=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(e=0;et);e++);let r=0===e?0:i[e-1],s=(t-r)/((ei)continue;let f=d-u;f<3&&(f=3,u--);const p=f/2,g=p/this.sinTheta,m=this.cosTheta*g,b=u+p;let y,v,w;if(c?(y=this.height+m,v=Math.PI+Math.PI/2-this.theta,w=Math.PI+Math.PI/2+this.theta):(y=-m,v=Math.PI/2-this.theta,w=Math.PI/2+this.theta),this.showBlocks&&"all"!==t.chr){const i=(t.start1-o)/a,n=(t.end1-o)/a,r=(t.start2-o)/a,l=(t.end2-o)/a,h=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(i,s,n-i,h),e.fillRect(r,s,l-r,h)}n&&!this.config.useScore&&f>r&&(n=kf(n,this.alpha)),e.strokeStyle=n,e.fillStyle=n,e.beginPath(),e.arc(b,y,g,v,w,!1),e.stroke(),t.drawState={xc:b,yc:y,r:g}}else{let r=Math.round((t.start-o)/a),s=Math.round((t.end-o)/a);if(s<0||r>i)continue;let l=s-r;l<3&&(l=3,r--);const h=t.chr===t.chr1?t.chr2:t.chr1;e.strokeStyle=n,e.fillStyle=kf(Zd(h),.5),c?(e.fillRect(r,this.height/2,l,this.height/2),e.fillText(h,r+l/2,this.height/2-5),t.drawState={x:r,y:this.height/2,w:l,h:this.height/2}):(e.fillRect(r,0,l,this.height/2),e.fillText(h,r+l/2,this.height/2+13),t.drawState={x:r,y:0,w:l,h:this.height/2})}}}var h}getScaleFactor(t,e,i,n){return n?i/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):i/(e-t)}drawProportional(t){const e=t.context,i=t.pixelWidth,n=t.pixelHeight,r=t.bpPerPixel,s=t.bpStart,o=r,a=t.referenceFrame.start,l=t.referenceFrame.end;na.fillRect(e,0,t.pixelTop,i,n,{fillStyle:"rgb(255, 255, 255)"});const h=t.features;if(h&&h.length>0){const n=0,r=this.getScaleFactor(n,this.dataRange.max,t.pixelHeight-1,this.logScale),c=this.arcOrientation?t.pixelHeight:0;for(let t of h){t.drawState=void 0;const n=this.valueColumn?t[this.valueColumn]:t.score;if(void 0===n||Number.isNaN(n))continue;const h=Math.round((this.logScale?Math.log10(n+1):n)*r);if(t.chr1===t.chr2||"all"===t.chr){const{m1:i,m2:r}=wf(t,this.browser.genome);let u=Math.round((i-s)/o),d=Math.round((r-s)/o)-u;if(d<3&&(d=3,u--),nthis.dataRange.max)continue;if("proportional"!==this.arcType){const t="partialInView"===this.arcType,e=i>=a&&r<=l;let n=!1,s=!1;if(!e&&t&&(n=a<=i&&i<=l,n||(s=a<=r&&r<=l)),!(e||n||s))continue}const f=d/2,p=u+d/2;t.drawState={xc:p,yc:c,radiusX:f,radiusY:h};const g=!!this.arcOrientation,m=t.color||this.color;if(e.strokeStyle=m,e.lineWidth=t.thickness||this.thickness||1,!0===e.isSVG?e.strokeEllipse(p,c,f,h,0,0,Math.PI,g):(e.beginPath(),e.ellipse(p,c,f,h,0,0,Math.PI,g),e.stroke()),this.alpha&&(e.fillStyle=kf(m,this.alpha),!0===e.isSVG?e.fillEllipse(p,c,f,h,0,0,Math.PI,g):e.fill()),this.showBlocks&&"all"!==t.chr){e.fillStyle=m;const i=(t.start1-s)/o,n=(t.end1-s)/o,r=(t.start2-s)/o,a=(t.end2-s)/o,l=this.arcOrientation?-this.blockHeight:this.blockHeight;e.fillRect(i,c,n-i,l),e.fillRect(r,c,a-r,l)}}else{let r=Math.round((t.start-s)/o),a=Math.round((t.end-s)/o);if(a<0||r>i||nthis.dataRange.max)continue;const l=Math.min(h,this.height-13);let c=a-r;c<3&&(c=3,r--);const u=t.chr===t.chr1?t.chr2:t.chr1;if(e.font="8px sans-serif",e.textAlign="center",e.fillStyle=kf(Zd(u),.5),this.arcOrientation){const i=this.height-l;e.fillRect(r,i,c,l),e.fillText(u,r+c/2,i-5),t.drawState={x:r,y:i,w:c,h:l}}else e.fillRect(r,0,c,l),e.fillText(u,r+c/2,l+13),t.drawState={x:r,y:0,w:c,h:l}}}}}clearAxis(t,e,i){na.fillRect(t,0,0,e,i,{fillStyle:"rgb(255, 255, 255)"})}paintAxis(t,e,i){const n={min:0,max:this.dataRange.max};"proportional"===this.arcType||"inView"===this.arcType||"partialInView"===this.arcType?(this.painter.flipAxis=!this.arcOrientation,this.painter.dataRange=n,this.painter.paintAxis(t,e,i)):this.clearAxis(t,e,i)}menuItemList(){let t=[];if(this.hasValue){t.push("
");const e={nested:"Nested",proportional:"Proportional - All",inView:"Proportional - Both Ends in View",partialInView:"Proportional - One End in View"};t.push("Arc Type");for(let i of["nested","proportional","inView","partialInView"])t.push({object:fe(zi(e[i],i===this.arcType)),click:()=>{this.arcType=i,this.trackView.repaintViews()}})}return t.push("
"),t.push({name:"Toggle arc direction",click:()=>{this.arcOrientation=!this.arcOrientation,this.trackView.repaintViews()}}),t.push({name:this.showBlocks?"Hide Blocks":"Show Blocks",click:()=>{this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),"proportional"!==this.arcType&&"inView"!==this.arcType&&"partialInView"!==this.arcType||(t=t.concat(Ui.numericDataMenuItems(this.trackView))),this.browser.circularView&&(t.push("
"),t.push({label:"Add interactions to circular view",click:()=>{for(let t of this.trackView.viewports)this.addChordsForViewport(t.referenceFrame)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,i=[];return i.push({label:"Add interactions to circular view",click:()=>{const t=e.referenceFrame;this.addChordsForViewport(t)}}),i.push("
"),i}}addChordsForViewport(t){const e=("all"===t.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end)).filter((t=>t.drawState));0!==e.length&&_d(e.map((t=>{const e=t._f||t;return{uniqueId:`${e.chr1}:${e.start1}-${e.end1}_${e.chr2}:${e.start2}-${e.end2}`,refName:vd(e.chr1),start:e.start1,end:e.end1,mate:{refName:vd(e.chr2),start:e.start2,end:e.end2}}})),this,t,.5)}doAutoscale(t){let e=0;if(t)for(let i of t){const t=this.valueColumn?i[this.valueColumn]:i.score;Number.isNaN(t)||(e=Math.max(e,t))}return{min:0,max:e}}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=[];for(let t of e){const e=t._||t;if(i.push({name:"Region 1",value:_f(e.chr1,e.start1,e.end1,e.strand1)}),i.push({name:"Region 2",value:_f(e.chr2,e.start2,e.end2,e.strand2)}),e.name&&i.push({name:"Name",value:e.name}),void 0!==e.value&&i.push({name:"Value",value:e.value}),void 0!==e.score&&i.push({name:"Score",value:e.score}),e.extras&&this.header&&this.header.columnNames){const t=this.header.columnNames,n=this.header.hiccups?6:10;for(let r=n;r=e-a&&t.canvasX<=e+s+a&&t.canvasY>=n&&t.canvasY<=n+o){const n=-Math.abs(t.canvasX-(e+s/2));i.push({score:n,feature:r});break}}}return i.length>1&&i.sort(((t,e)=>t.score-e.score)),i.map((t=>t.feature))}}function wf(t,e){let i=(t.start1+t.end1)/2,n=(t.start2+t.end2)/2;if("all"===t.chr&&(i=e.getGenomeCoordinate(t.chr1,i),n=e.getGenomeCoordinate(t.chr2,n)),i>n){const t=i;i=n,n=t}return{m1:i,m2:n}}function _f(t,e,i,n){return n&&"."!==n?`${t}:${$i(e+1)}-${$i(i)} (${n})`:`${t}:${$i(e+1)}-${$i(i)}`}const xf=new Map;function kf(t,e){const i=`${t}_${e}`;let n=xf.get(i);return n||(n=xo.addAlpha(t,e),xf.set(i,n)),n}function Sf(t){const e=t=>{const e=Object.assign({},t);return e.chr="all",e.start=i.getGenomeCoordinate(t.chr1,t.start1),e.end=i.getGenomeCoordinate(t.chr2,t.end2),e},i=this.genome;let n,r=0;for(let e of i.wgChromosomeNames){let i=t[e];if(i)for(let t of i)t.dup||(r++,t.score&&(!n||t.score>n.score)&&(n=t))}const s=this.maxWGCount,o=n&&n.score>0&&r>s?5:1,a=Math.floor(s/o),l=n&&n.score>0?Math.log(n.score)/o:Number.MAX_SAFE_INTEGER;let h,c=[],u=[];for(let t=0;tt.name)):[]}return this.header}getCallsetsLength(){return this.callSets?this.callSets.length:0}async getFeatures(t,e,i,n){return void 0===this.header&&(this.header=await this.getHeader()),this.featureSource.getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow})}hasSamples(){return this.getCallsetsLength()>0}getSamples(){return{yOffset:this.sampleYOffset,names:this.sampleNames,height:this.sampleHeight}}computePixelHeight(t){if(!t||0==t.length)return 10;const e="COLLAPSED"===this.displayMode?1:this.nVariantRows,i="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,n="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,r="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight;return 10+e*(n+i)+i+(1+(!1===this.showGenotypes?0:this.getCallsetsLength()*e))*(r+i)}variantRowCount(t){this.nVariantRows=t}draw({context:t,pixelWidth:e,pixelHeight:i,bpPerPixel:n,bpStart:r,pixelTop:s,features:o}){na.fillRect(t,0,s,e,i,{fillStyle:"rgb(255, 255, 255)"});const a="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,l="COLLAPSED"===this.displayMode?1:this.nVariantRows,h="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=10+l*(h+a);let c=this.callSets;!c&&this._f&&(c=this._f.callSets);const u=this.getCallsetsLength();if(c&&u>0&&!1!==this.showGenotypes&&na.strokeLine(t,0,this.variantBandHeight,e,this.variantBandHeight,{strokeStyle:"rgb(224,224,224) "}),o){const i="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,a=r+e*n+1;for(let e of o){if(e.enda)break;const o="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,l=10+("COLLAPSED"===this.displayMode?0:e.row*(o+s)),h=o;let d=Math.round((e.start-r)/n),f=Math.round((e.end-r)/n),p=Math.max(1,f-d);p<3?(p=3,d-=1):p>5&&(d+=1,p-=2),t.fillStyle=this.getColorForFeature(e),t.fillRect(d,l,p,h);let g=this.getVariantStrokecolor(e);if(g&&(t.strokeStyle=g,t.strokeRect(d,l,p,h)),this.callContextHook(e,t,d,l,p,h),e.pixelRect={x:d,y:l,w:p,h},u>0&&!1!==this.showGenotypes){const n="COLLAPSED"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+s,this.sampleHeight=n*(i+s);let r=0;if(c&&e.calls)for(let n of c){const o=e.calls[n.id];if(o){const a="COLLAPSED"===this.displayMode?0:e.row,l=this.sampleYOffset+r*this.sampleHeight+a*(i+s);let h=!0,c=!0,u=!1;if(o.genotype)for(let t of o.genotype){if("."===t){u=!0;break}0!==t&&(c=!1),0===t&&(h=!1)}o.genotype?t.fillStyle=u?this.noCallColor:c?this.homrefColor:h?this.homvarColor:this.hetvarColor:t.fillStyle=this.noGenotypeColor,t.fillRect(d,l,p,i),n.pixelRect={x:d,y:l,w:p,h:i}}r++}}}}else console.log("No feature list")}getColorForFeature(t){const e=t._f||t;let i;if(this.colorBy){const t=this.colorBy;let n;e.info.hasOwnProperty(t)?n=e.info[t]:Tf.has(t)&&(n=e[Tf.get(t)]),i=this.getVariantColorTable(t).getColor(n),i||(i="gray")}else i=this._color?"function"==typeof this._color?this._color(t):this._color:"NONVARIANT"===e.type?this.nonRefColor:"MIXED"===e.type?this.mixedColor:this.color;return i}getVariantStrokecolor(t){const e=t._f||t;let i;return i=this._strokecolor?"function"==typeof this._strokecolor?this._strokecolor(e):this._strokecolor:void 0,i}callContextHook(t,e,i,n,r,s){if(this._context_hook&&"function"==typeof this._context_hook){const o=t._f||t;e.save(),this._context_hook(o,e,i,n,r,s),e.restore()}}clickedFeatures(t){let e=super.clickedFeatures(t);const i="EXPANDED"===this.displayMode?this.expandedVGap:this.squishedVGap,n=i+("SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),r=t.y;if(r<=this.variantBandHeight){const t="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=Math.floor((r-10)/(t+i));"COLLAPSED"!==this.displayMode&&(e=e.filter((t=>t.row===n)))}else if(this.callSets){const t=this.callSets,i=r-this.variantBandHeight,s=Math.floor(i/this.sampleHeight);if(s>=0&&st.row===r)),a=t[s];e=o.map((t=>{const e=t.calls[a.id];return function(t,e){if(t.genotype){let i="";if("."===e.alternateBases)i="No Call";else{const n=e.alternateBases.split(",");for(let r of t.genotype)i.length>0&&(i+="|"),i+="."===r?".":0===r?e.referenceBases:n[r-1].replace("<","<")}t.genotypeName=i}}(e,t),e}))}}return e}popupData(t,e){void 0===e&&(e=this.clickedFeatures(t));const i=t.genomicLocation,n=this.browser.genome.id,r=this.browser.sampleInformation;let s=[];for(let t of e){const e=t._f||t;if(s.length>0&&s.push({html:'
'}),"function"==typeof e.popupData){const t=e.popupData(i,n);Array.prototype.push.apply(s,t)}else{const t=e;if(void 0!==t.callSetName&&s.push({name:"Name",value:t.callSetName}),t.genotypeName&&s.push({name:"Genotype",value:t.genotypeName}),void 0!==t.phaseset&&s.push({name:"Phase set",value:t.phaseset}),void 0!==t.genotypeLikelihood&&s.push({name:"genotypeLikelihood",value:t.genotypeLikelihood.toString()}),r){var o=r.getAttributes(t.callSetName);o&&Object.keys(o).forEach((function(t){var e=t.replace(/([A-Z])/g," $1");e=e.charAt(0).toUpperCase()+e.slice(1),s.push({name:e,value:o[t]})}))}var a=Object.keys(t.info);a.length&&s.push("
"),a.forEach((function(e){s.push({name:e,value:decodeURIComponent(t.info[e])})}))}}return s}menuItemList(){const t=[];if(this.header.INFO&&this.header.INFO){const e=this.header.INFO.SVTYPE?["SVTYPE"]:[];if(this._initColorBy&&"SVTYPE"!==this._initColorBy&&e.push(this._initColorBy),e.length>0){t.push("
");const i=fe('
');i.text("Color by:"),t.push({name:void 0,object:i,click:void 0,init:void 0}),e.sort();for(let i of e){const e=this.colorBy===i,n=i||"None";t.push(this.colorByCB({key:i,label:n},e))}t.push(this.colorByCB({key:void 0,label:"None"},void 0===this.colorBy)),t.push("
")}}this.getCallsetsLength()>0&&(t.push({object:fe('
')}),t.push({object:fe(zi("Show Genotypes",this.showGenotypes)),click:()=>{this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),t.push({object:fe('
')});for(let e of["COLLAPSED","SQUISHED","EXPANDED"])t.push({object:fe(zi({COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"}[e],e===this.displayMode)),click:()=>{this.displayMode=e,this.trackView.checkContentHeight(),this.trackView.repaintViews()}});return this.browser.circularView&&(t.push("
"),t.push({label:"Add SVs to circular view",click:()=>{for(let t of this.trackView.viewports)this.sendChordsForViewport(t)}})),t}contextMenuItemList(t){if(this.browser.circularView){const e=t.viewport,i=[];return i.push({label:"Add SVs to Circular View",click:()=>{this.sendChordsForViewport(e)}}),i.push("
"),i}}sendChordsForViewport(t){const e=t.referenceFrame;let i;if("all"===e.chr){const t=this.featureSource.getAllFeatures(),e=Object.keys(t).map((e=>t[e]));i=[].concat(...e)}else i=this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end);_d(i.filter((t=>{const e=t._f||t;return e.info&&e.info.CHR2&&e.info.END&&(e.info.CHR2!==e.chr||Math.abs(Number.parseInt(e.info.END)-e.pos)>1e6)})).map((t=>{const e=t._f||t,i=Number.parseInt(e.info.END),n=i-100,r=i+100;return{uniqueId:`${e.chr}:${e.start}-${e.end}_${e.info.CHR2}:${e.info.END}`,refName:vd(e.chr),start:e.start,end:e.end,mate:{refName:vd(e.info.CHR2),start:n,end:r}}})),this,e,.5)}colorByCB(t,e){return{name:void 0,object:fe(zi(t.label,e)),click:()=>{t.key===this.colorBy?(this.colorBy=void 0,delete this.config.colorBy,this.trackView.repaintViews()):(this.colorBy=t.key,this.config.colorBy=t.key,this.trackView.repaintViews())},init:void 0}}getState(){const t=super.getState();return this._color&&"function"!=typeof this._color&&(t.color=this._color),t}getVariantColorTable(t){if(this.colorTables||(this.colorTables=new Map),!this.colorTables.has(t)){let e;e="SVTYPE"===t?Ef:new ta("Set1"),this.colorTables.set(t,e)}return this.colorTables.get(t)}}const Ef=new ea({DEL:"#ff2101",INS:"#001888",DUP:"#028401",INV:"#008688",CNV:"#8931ff",BND:"#891100","*":"#002eff"});class Mf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.name=t.name,this.pValueField=t.pValueField||"pValue",this.geneField=t.geneField||"geneSymbol",this.snpField=t.snpField||"snp";const e=t.minLogP||t.min,i=t.maxLogP||t.max;this.dataRange={min:e||3.5,max:i||25},this.autoscale=!i||t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||2,this.height=t.height||100,this.autoHeight=!1,this.disableButtons=t.disableButtons,this.visibilityWindow=void 0===t.visibilityWindow?2e6:t.visibilityWindow>=0?Math.min(2e6,t.visibilityWindow):2e6,this.featureSource=$c(t,this.browser.genome),Sd.gtexLoaded=!0}paintAxis(t,e,i){const n=(this.dataRange.max-this.dataRange.min)/i,r={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};na.fillRect(t,0,0,e,i,{fillStyle:"rgb(255, 255, 255)"});const s=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let o=4;o<=this.dataRange.max;o+=s){const s=.85*e,a=s-5,l=s,h=i-(o-this.dataRange.min)/n;na.strokeLine(t,a,h,l,h,r),h>8&&na.fillText(t,o,a-1,h+2,r)}r.textAlign="center",na.fillText(t,"-log10(pvalue)",e/4,i/2,r,{rotate:{angle:-90}})}async getFeatures(t,e,i){const n=this.pValueField,r=this.visibilityWindow,s=await this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:r});return s.forEach((function(t){t.value=t[n]})),s}draw(t){const e=t.context,i=t.pixelWidth,n=t.pixelHeight;this.background&&na.fillRect(e,0,0,i,n,{fillStyle:this.background}),na.strokeLine(e,0,n-1,i,n-1,{strokeStyle:this.divider});const r=r=>{const s=r?2*this.dotSize:this.dotSize,o=t.bpStart,a=(this.dataRange.max-this.dataRange.min)/n,l=t.referenceFrame.selection;for(let c of t.features){const u=(c.start-o+.5)/t.bpPerPixel;if(u<0)continue;if(u>i)break;const d=c.snp.toUpperCase(),f=c[this.geneField].toUpperCase(),p=l&&(l.snp===d||l.gene===f);if(!r||p){l&&l.snp===d&&l.addGene(f);var h=-Math.log(c[this.pValueField])/Math.LN10;if(h>=this.dataRange.min){let t;h>this.dataRange.max?(h=this.dataRange.max,t=!0):t=!1;const i=Math.max(0+s,n-Math.round((h-this.dataRange.min)/a));let o;c.px=u,c.py=i,c.radius=s,r&&l?(o=l.colorForGene(f),na.setProperties(e,{fillStyle:o,strokeStyle:"black"})):(o=t?"rgb(150, 150, 150)":"rgb(180, 180, 180)",na.setProperties(e,{fillStyle:o,strokeStyle:o})),na.fillCircle(e,u,i,s),na.strokeCircle(e,u,i,s)}}}};r(!1),r(!0)}popupData(t,e){if(void 0===e&&(e=t.viewport.cachedFeatures),!e||0===e.length)return[];const i=this.name,n=[];for(let r of e)Math.abs(r.px-t.canvasX)0&&n.push("
"),n.push({name:"snp id",value:r.snp},{name:"gene id",value:r.geneId},{name:"gene name",value:r.geneName},{name:"p value",value:r.pValue},{name:"tissue",value:i}));return n}menuItemList(){return Ui.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){var e=t.map((function(t){return-Math.log(t.value)/Math.LN10}));this.dataRange.max=function(t,e){if(0!==t.length){var i=Math.floor(t.length*((100-e)/100));return 0===i?(t.sort((function(t,e){return e-t})),t[i]):function(t,e){var i,n=new wo;for(i=0;in.content[0])&&(n.content.length===e&&n.pop(),n.push(r))}return n.content[0]}(t,i)}}(e,this.autoscalePercentile)}else{const t=this.config.maxLogP||this.config.max;this.dataRange.max=t||25}return this.dataRange}}const Rf={X:"rgb(204, 153, 0)",Y:"rgb(153, 204, 0)",Un:"darkGray)",1:"rgb(80, 80, 255)",2:"rgb(206, 61, 50)","2a":"rgb(210, 65, 55)","2b":"rgb(215, 70, 60)",3:"rgb(116, 155, 88)",4:"rgb(240, 230, 133)",5:"rgb(70, 105, 131)",6:"rgb(186, 99, 56)",7:"rgb(93, 177, 221)",8:"rgb(128, 34, 104)",9:"rgb(107, 215, 107)",10:"rgb(213, 149, 167)",11:"rgb(146, 72, 34)",12:"rgb(131, 123, 141)",13:"rgb(199, 81, 39)",14:"rgb(213, 143, 92)",15:"rgb(122, 101, 165)",16:"rgb(228, 175, 105)",17:"rgb(59, 27, 83)",18:"rgb(205, 222, 183)",19:"rgb(97, 42, 121)",20:"rgb(174, 31, 99)",21:"rgb(231, 199, 111)",22:"rgb(90, 101, 94)",23:"rgb(204, 153, 0)",24:"rgb(153, 204, 0)",25:"rgb(51, 204, 0)",26:"rgb(0, 204, 51)",27:"rgb(0, 204, 153)",28:"rgb(0, 153, 204)",29:"rgb(10, 71, 255)",30:"rgb(71, 117, 255)",31:"rgb(255, 194, 10)",32:"rgb(255, 209, 71)",33:"rgb(153, 0, 51)",34:"rgb(153, 26, 0)",35:"rgb(153, 102, 0)",36:"rgb(128, 153, 0)",37:"rgb(51, 153, 0)",38:"rgb(0, 153, 26)",39:"rgb(0, 153, 102)",40:"rgb(0, 128, 153)",41:"rgb(0, 51, 153)",42:"rgb(26, 0, 153)",43:"rgb(102, 0, 153)",44:"rgb(153, 0, 128)",45:"rgb(214, 0, 71)",46:"rgb(255, 20, 99)",47:"rgb(0, 214, 143)",48:"rgb(20, 255, 177)"};for(let Sy of Object.keys(Rf))Rf["chr"+Sy]=Rf[Sy];for(let Cy=1;Cy<=48;Cy++){if(10===Cy)continue;const Ay=Lf(Cy);Rf[Ay]=Rf[Cy.toString()]}function Lf(t){if(!+t)return!1;for(var e=String(+t).split(""),i=["","C","CC","CCC","CD","D","DC","DCC","DCCC","CM","","X","XX","XXX","XL","L","LX","LXX","LXXX","XC","","I","II","III","IV","V","VI","VII","VIII","IX"],n="",r=3;r--;)n=(i[+e.pop()+10*r]||"")+n;return Array(+e.join("")+1).join("M")+n}class Bf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.useChrColors=void 0===t.useChrColors||t.useChrColors,this.trait=t.trait,this.posteriorProbability=t.posteriorProbability,this.valueProperty="bed"===t.format?"score":"value",this.height=t.height||100,this.autoscale=t.autoscale,this.autoscalePercentile=void 0===t.autoscalePercentile?98:t.autoscalePercentile,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||3,this.popoverWindow=void 0===t.popoverWindow?1e8:t.popoverWindow,this.useChrColors?this.colorScale=new ea(t.colorTable||Rf):t.color?this.colorScale=new pf(t.color):this.colorScale=new df(t.colorScale||{thresholds:[5e-8,5e-4,.5],colors:["rgb(255,50,50)","rgb(251,100,100)","rgb(251,170,170)","rgb(227,238,249)"]}),this.featureSource=$c(t,this.browser.genome)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(t,e,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:n})}draw(t){const e=t.features,i=t.context,n=t.pixelWidth,r=t.pixelHeight;if(this.background&&na.fillRect(i,0,0,n,r,{fillStyle:this.background}),na.strokeLine(i,0,r-1,n,r-1,{strokeStyle:this.divider}),e){const s=t.bpPerPixel,o=t.bpStart,a=o+n*s+1;for(let t of e){const e=t.start;if(ea)break;let n;if(this.posteriorProbability)n=t[this.valueProperty];else{const e=t[this.valueProperty];if(!e)continue;n=-Math.log10(e)}const l=this.useChrColors?t._f?t._f.chr:t.chr:n,h=this.colorScale.getColor(l),c=(this.dataRange.max-this.dataRange.min)/r,u=Math.round((e-o)/s),d=Math.max(this.dotSize,r-Math.round((n-this.dataRange.min)/c));h&&na.setProperties(i,{fillStyle:h,strokeStyle:"black"}),na.fillCircle(i,u,d,this.dotSize),t.px=u,t.py=d}}}paintAxis(t,e,i){na.fillRect(t,0,0,e,i,{fillStyle:"rgb(255, 255, 255)"});var n={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"};const r=(this.dataRange.max-this.dataRange.min)/i;if(this.posteriorProbability){const e=.1;for(let s=this.dataRange.min;s0&&i.push("
"),5==r){i.push("...");break}if("function"==typeof s.popupData)i=i.concat(s.popupData());else{const t=s.realChr||s.chr,e=(s.realStart||s.start)+1;i.push({name:"chromosome",value:t}),i.push({name:"position",value:e}),i.push({name:"name",value:s.name}),n.posteriorProbability?i.push({name:"posterior probability",value:a}):i.push({name:"pValue",value:a})}r++}}}return i}menuItemList(){return Ui.numericDataMenuItems(this.trackView)}doAutoscale(t){if(t.length>0){const e=this.valueProperty,i=this.posteriorProbability,n=t.map((function(t){const n=t[e];return{value:i?n:-Math.log(n)/Math.LN10}}));this.dataRange=ha(n)}else this.posteriorProbability?this.dataRange={min:this.config.min||0,max:this.config.max||1}:this.dataRange={min:this.config.max||25,max:this.config.min||0};return this.dataRange}}class Nf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.autoscale=t.autoscale||void 0===t.max,this.dataRange={min:t.min||0,max:t.max},this.windowFunction=t.windowFunction||"mean",this.paintAxis=$u,this.graphType=t.graphType||"bar",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=$c(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if("function"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleNames=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty("clickToHighlight")){let t=this.header.clickToHighlight;this.config.clickToHighlight=t,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty("highlight")){this.config.highlightSamples={};let t=this.header.highlight;Array.isArray(t)||(t=[t]);for(let e of t){const t=e.split(";");2===t.length&&(this.config.highlightSamples[t[0]]=t[1])}}}}menuItemList(){return Ui.numericDataMenuItems(this.trackView)}async getFeatures(t,e,i){const n=await this.featureSource.getFeatures({chr:t,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let r,s;for(let t=1;te&&(r=t-1),void 0===s&&n[t].start>i){s=t+1;break}return void 0===r&&(r=0),void 0===s&&(s=n.length),n.slice(r,s)}draw(t){const{features:e,context:i,bpPerPixel:n,bpStart:r,pixelWidth:s,pixelHeight:o}=t,a=t=>(this.dataRange.max-t)/(this.dataRange.max-this.dataRange.min)*o,l=function(t){let e=Math.floor((t-r)/n);return isNaN(e)&&console.warn("isNaN(x). feature start "+$i(t)+" bp start "+$i(r)),e};if(e&&e.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const t=this.config.highlightSamples,n=this.config.onlyHandleClicksForHighlightedSamples,r=this.config.clickToHighlight;let s=-1,o={},h=[],c=[];this.clickDetectorCache={};for(let u of e){const e=l(u.start),d=l(u.end),f=s>=0?l(s):e;if(!isNaN(e)&&!isNaN(d)){this.clickDetectorCache[e]=[],this.clickDetectorCache[d]=[];for(let s=0;s=1){const s=o[l],c=a(s),u=t&&t[l];u?h.push([f,c,e,g,u]):r&&l in this.config.samplesClickedToHighlight?h.push([f,c,e,g,this.config.samplesClickedToHighlight[l]]):na.strokeLine(i,f,c,e,g,{strokeStyle:"#D9D9D9"}),n&&!(l in t)||this.clickDetectorCache[e].push([f,c,e,g,l,u||"gray"])}if(d-e>=1){const s=t&&t[l];s?c.push([e,g,d,g,s]):r&&l in this.config.samplesClickedToHighlight?c.push([e,g,d,g,this.config.samplesClickedToHighlight[l]]):na.strokeLine(i,e,g,d,g,{strokeStyle:"gray"}),n&&!(l in t)||this.clickDetectorCache[d].push([e,g,d,g,l,s||"gray"])}o[l]=p}s=u.end}}for(let t of h)na.strokeLine(i,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:1.3});for(let t of c)na.strokeLine(i,t[0],t[1],t[2],t[3],{strokeStyle:t[4],lineWidth:2})}(t=>{if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let i=a(e.y),n={strokeStyle:e.color,strokeWidth:2};e.dotted?na.dashedLine(t.context,0,i,t.pixelWidth,i,5,n):na.strokeLine(t.context,0,i,t.pixelWidth,i,n)}})(t)}doAutoscale(t){let e,i;return t.length>0?(e=Number.MAX_VALUE,i=-Number.MAX_VALUE,t.forEach((function(t){e=Math.min(e,...t.values),i=Math.max(i,...t.values)})),e-=.01,i+=.01):(e=0,i=100),{min:e,max:i}}clickedFeatures(t){const e=t.canvasX,i=t.canvasY;let n=null;for(n of Object.keys(this.clickDetectorCache))if(n=parseInt(n),n>=e)break;if(n){let t=Number.MAX_VALUE,o=[];const a=this.clickDetectorCache[n];for(let n of a){const r=n[0],s=n[2];if(es)return[];const a=n[1],l=n[3];if(iMath.max(a,l)+10)continue;const h=Ff(e,i,r,a,s,l);h0?l/h:0}class Of extends ch{constructor(t,e){super(t,e),t.height||(this.height=300),this.arcOrientation=!1,this.theta=Math.PI/2,"bp"===t.format?this.featureSource=new Pf(t,e.genome):this.featureSource=new bc(t,e.genome)}async getFeatures(t,e,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:t,start:e,end:i,visibilityWindow:n})}draw(t){const e=t.context,i=Math.PI/2,n=t.pixelWidth,r=t.pixelHeight;t.viewportWidth;const s=t.bpPerPixel,o=t.bpStart,a=s,l=this.arcOrientation;na.fillRect(e,0,t.pixelTop,n,r,{fillStyle:"rgb(255, 255, 255)"});const h=t.features;if(h){Df(h,1);for(let t of h)if(t.startLeft){let n=Math.round((t.startLeft-o)/a),r=Math.round((t.startRight-o)/a),s=Math.round((t.endLeft-o)/a),h=Math.round((t.endRight-o)/a);e.fillStyle=t.color,e.strokeStyle=t.color,e.beginPath();let c=(n+h)/2,u=(h-n)/2,d=this.height,f=Math.PI+(Math.PI/2-i),p=2*Math.PI-(Math.PI/2-i);l?(d=0,e.arc(c,d,u,p,f),e.lineTo(h,d)):(e.arc(c,d,u,f,p),e.lineTo(s,d));const g=(r+s)/2,m=(s-r)/2,b=d;l?(e.arc(g,b,m,f,p,!0),e.lineTo(s,b)):(e.arc(g,b,m,p,f,!0),e.lineTo(n,b)),e.stroke(),e.fill(),t.drawState={x1:c,y1:d,r1:u,x2:g,y2:b,r2:m,sa:f,ea:p}}else{let n=Math.round((t.start-o)/a),r=Math.round((t.end-o)/a);e.strokeStyle=t.color,e.beginPath();let s=(n+r)/2,h=(r-n)/2,c=this.height,u=Math.PI+(Math.PI/2-i),d=2*Math.PI-(Math.PI/2-i);l?(c=0,e.arc(s,c,h,d,u)):e.arc(s,c,h,u,d),e.stroke(),t.drawState={x1:s,y1:c,r1:h,sa:u,ea:d}}}}clickedFeatures(t){const e=super.clickedFeatures(t),i=[];Df(e,-1);for(let n of e){const e=n.drawState,r=t.canvasX-e.x1,s=t.canvasY-e.y1,o=Math.sqrt(r*r+s*s),a=e.r1+3;let l,h;if(void 0===e.x2)l=o,h=e.r1-3;else{const i=t.canvasX-e.x2,n=t.canvasY-e.y2;l=Math.sqrt(i*i+n*n),h=e.r2-3}if(oh){i.push(n);break}}return i}popupData(t,e){if(void 0===e&&(e=this.clickedFeatures(t)),e&&e.length>0)return this.extractPopupData(e[0],this.getGenomeId())}menuItemList(){var t=this;return[{name:"Toggle arc direction",click:function(){t.arcOrientation=!t.arcOrientation,t.trackView.repaintViews()}}]}}function Df(t,e){t.sort((function(t,i){const n=void 0===t.score?-Number.MAX_VALUE:t.score,r=void 0===i.score?-Number.MAX_VALUE:i.score;return(void 0===e?1:e)*(n-r)}))}class Pf{constructor(t,e){this.config=t,this.genome=e}async getFeatures({chr:t,start:e,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(t,e,i);{const n=la(this.config),r=await zo.loadString(this.config.url,n);return this.featureCache=new Zo(function(t){if(!t)return null;const e=Hh(t);let i,n=!0;const r=[],s=[],o=[];for(;void 0!==(i=e.nextLine());){const t=i.split("\t");if(n&&i.startsWith("color:")){const e="rgb("+t[1]+","+t[2]+","+t[3]+")";r.push(e),t.length>4&&s.push(t[4])}else{n=!1;const e=t[0],i=Number.parseInt(t[1])-1,l=Number.parseInt(t[2])-1,h=Number.parseInt(t[3]),c=Number.parseInt(t[4]);var a=Number.parseInt(t[5]);const u=r[a];let d;d=i<=c?{chr:e,startLeft:Math.min(i,l),startRight:Math.max(i,l),endLeft:Math.min(h,c),endRight:Math.max(h,c),color:u,score:a}:{chr:e,startLeft:Math.min(h,c),startRight:Math.max(h,c),endLeft:Math.min(i,l),endRight:Math.max(i,l),color:u,score:a},d.start=d.startLeft,d.end=d.endRight,s.length>a&&(d.description=s[a]),o.push(d)}}return o}(r),s),this.featureCache.queryFeatures(t,e,i)}}}class zf{constructor(t){this.browser=t,this.type="ideogram",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}async getFeatures(t,e,i){return[]}computePixelHeight(t){return this.height}draw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n}){const r=e.chr,s=e.genome.getChromosome(r);if(void 0===s||i<=0||n<=0||"all"===r.toLowerCase())return;!function({ctx:t,chr:e,referenceFrame:i,genome:n,width:r,height:s,stainColors:o}){const a=.5;if(void 0===n)return;na.fillRect(t,0,0,r,s,{fillStyle:xo.greyScale(255)});const l=n.getCytobands(e);if(l){const e=0+s/2,i=[],n=[];if(0===l.length)return;const h=r/l[l.length-1].end;t.beginPath(),na.roundRect(t,a,.5,r-1,s-1,(s-1)/2,0,1),t.clip();for(let r=0;r0&&h[h.length-1].end&&(l=Math.max(l,h[h.length-1].end),s.bpLength=l),o{Vf.getColor(t)}));const Hf={};class jf extends ch{constructor(t,e){super(t,e)}init(t){super.init(t),this.type=t.type||"junctions",t._featureSource?(this.featureSource=t._featureSource,delete t._featureSource):this.featureSource=t.featureSource?t.featureSource:$c(t,this.browser.genome),this.margin=void 0===t.margin?10:t.margin,this.height||(this.height=100),void 0===t.colorByNumReadsThreshold&&(t.colorByNumReadsThreshold=5)}async postInit(){if("function"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&"function"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await 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e=0;for(;e<144;)t.lens[e++]=8;for(;e<256;)t.lens[e++]=9;for(;e<280;)t.lens[e++]=7;for(;e<288;)t.lens[e++]=8;for(Op(1,t.lens,0,288,Kp,0,t.work,{bits:9}),e=0;e<32;)t.lens[e++]=5;Op(2,t.lens,0,32,Jp,0,t.work,{bits:5}),rg=!1}t.lencode=Kp,t.lenbits=9,t.distcode=Jp,t.distbits=5},og=(t,e,i,n)=>{let r;const s=t.state;return null===s.window&&(s.wsize=1<=s.wsize?(s.window.set(e.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(e.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(e.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whaveng(t,15),inflateInit2:ng,inflate:(t,e)=>{let i,n,r,s,o,a,l,h,c,u,d,f,p,g,m,b,y,v,w,_,x,k,S=0;const C=new Uint8Array(4);let A,T;const I=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(!t||!t.state||!t.output||!t.input&&0!==t.avail_in)return 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t&&t.state?(n=t.state,0!==n.wrap&&11!==n.mode?jp:11===n.mode&&(r=1,r=wp(r,e,i,0),r!==n.check)?$p:(s=og(t,e,i,i),s?(n.mode=31,qp):(n.havedict=1,Up))):jp},inflateInfo:"pako inflate (from Nodeca project)"},lg=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name="",this.comment="",this.hcrc=0,this.done=!1},hg=Object.prototype.toString,{Z_NO_FLUSH:cg,Z_FINISH:ug,Z_OK:dg,Z_STREAM_END:fg,Z_NEED_DICT:pg,Z_STREAM_ERROR:gg,Z_DATA_ERROR:mg,Z_MEM_ERROR:bg}=Sp;function yg(t){this.options=Ap.assign({chunkSize:65536,windowBits:15,to:""},t||{});const e=this.options;e.raw&&e.windowBits>=0&&e.windowBits<16&&(e.windowBits=-e.windowBits,0===e.windowBits&&(e.windowBits=-15)),!(e.windowBits>=0&&e.windowBits<16)||t&&t.windowBits||(e.windowBits+=32),e.windowBits>15&&e.windowBits<48&&0==(15&e.windowBits)&&(e.windowBits|=15),this.err=0,this.msg="",this.ended=!1,this.chunks=[],this.strm=new Mp,this.strm.avail_out=0;let i=ag.inflateInit2(this.strm,e.windowBits);if(i!==dg)throw new Error(kp[i]);if(this.header=new lg,ag.inflateGetHeader(this.strm,this.header),e.dictionary&&("string"==typeof e.dictionary?e.dictionary=Ep.string2buf(e.dictionary):"[object ArrayBuffer]"===hg.call(e.dictionary)&&(e.dictionary=new Uint8Array(e.dictionary)),e.raw&&(i=ag.inflateSetDictionary(this.strm,e.dictionary),i!==dg)))throw new Error(kp[i])}function vg(t,e){const i=new yg(e);if(i.push(t),i.err)throw i.msg||kp[i.err];return i.result}yg.prototype.push=function(t,e){const i=this.strm,n=this.options.chunkSize,r=this.options.dictionary;let s,o,a;if(this.ended)return!1;for(o=e===~~e?e:!0===e?ug:cg,"[object ArrayBuffer]"===hg.call(t)?i.input=new Uint8Array(t):i.input=t,i.next_in=0,i.avail_in=i.input.length;;){for(0===i.avail_out&&(i.output=new Uint8Array(n),i.next_out=0,i.avail_out=n),s=ag.inflate(i,o),s===pg&&r&&(s=ag.inflateSetDictionary(i,r),s===dg?s=ag.inflate(i,o):s===mg&&(s=pg));i.avail_in>0&&s===fg&&i.state.wrap>0&&0!==t[i.next_in];)ag.inflateReset(i),s=ag.inflate(i,o);switch(s){case gg:case mg:case pg:case bg:return this.onEnd(s),this.ended=!0,!1}if(a=i.avail_out,i.next_out&&(0===i.avail_out||s===fg))if("string"===this.options.to){let t=Ep.utf8border(i.output,i.next_out),e=i.next_out-t,r=Ep.buf2string(i.output,t);i.next_out=e,i.avail_out=n-e,e&&i.output.set(i.output.subarray(t,t+e),0),this.onData(r)}else this.onData(i.output.length===i.next_out?i.output:i.output.subarray(0,i.next_out));if(s!==dg||0!==a){if(s===fg)return s=ag.inflateEnd(this.strm),this.onEnd(s),this.ended=!0,!0;if(0===i.avail_in)break}}return!0},yg.prototype.onData=function(t){this.chunks.push(t)},yg.prototype.onEnd=function(t){t===dg&&("string"===this.options.to?this.result=this.chunks.join(""):this.result=Ap.flattenChunks(this.chunks)),this.chunks=[],this.err=t,this.msg=this.strm.msg};var wg={Inflate:yg,inflate:vg,inflateRaw:function(t,e){return(e=e||{}).raw=!0,vg(t,e)},ungzip:vg,constants:Sp},{Inflate:_g,inflate:xg,inflateRaw:kg,ungzip:Sg}=wg,Cg=xg,Ag=Sg,Tg=new Map([[1,function(t,e){let i=new Uint8Array(t);return Cg(i).buffer}],[2,function(t,e){let i=t.byteLength,n=new Uint8Array(i),r=Math.floor(i/e),s=new DataView(t);for(var o=0;oHH",t,i);if(r!=(a%=65535)||s!=(l%=65535))throw'ValueError("fletcher32 checksum invalid")'}(t),t.slice(0,-4)}]]),Ig=class{constructor(t,e){this.fh=t,this.offset=e,this.depth=null}async init(){this.all_nodes=new Map,await this._read_root_node(),await this._read_children()}async _read_children(){let t=this.depth;for(;t>0;){for(var e of this.all_nodes.get(t))for(var i of e.get("addresses"))this._add_node(await this._read_node(i,t-1));t--}}async _read_root_node(){let t=await this._read_node(this.offset,null);this._add_node(t),this.depth=t.get("node_level")}_add_node(t){let e=t.get("node_level");this.all_nodes.has(e)?this.all_nodes.get(e).push(t):this.all_nodes.set(e,[t])}async _read_node(t,e){let i=await this._read_node_header(t,e);return i.set("keys",[]),i.set("addresses",[]),i}async _read_node_header(t){throw"NotImplementedError: must define _read_node_header in implementation class"}},Eg=class extends Ig{B_LINK_NODE=new Map([["signature","4s"],["node_type","B"],["node_level","B"],["entries_used","H"],["left_sibling","Q"],["right_sibling","Q"]]);async _read_node_header(t,e){let i=await Zf(this.B_LINK_NODE,this.fh,t);if(null!=e&&i.get("node_level")!=e)throw"node level does not match";return i}},Mg=class extends Eg{NODE_TYPE=0;constructor(t,e){super(t,e),this.ready=this.init()}async _read_node(t,e){let i=await this._read_node_header(t,e);t+=Xf(this.B_LINK_NODE);let n=[],r=[],s=i.get("entries_used");for(var o=0;o=0&&v[x]>=t[x];x--)v[x]=0,y[x]=b[x],x>0&&(v[x-1]+=1,y[x-1]+=1);if(y.slice(0,-1).every((function(t,i){return t=0;o--){if(e&1<0?r*=n:r=n}}return s}_nrecords_max(t,e,i){return Math.floor((t-10-i)/(e+i))}_required_bytes(t){return Math.ceil(np(t)/8)}_int_format(t){return["0&&(c=(await ep.unpack_from_async(a,this.fh,i))[0],i+=r),l.push([n,h,c])}}return s.set("keys",a),s.set("addresses",l),s}async _read_node_header(t,e){let i=await Zf(this.B_LINK_NODE,this.fh,t);return i.set("node_level",e),i}*iter_records(){for(let t of this.all_nodes.values())for(let e of t)for(let t of e.get("keys"))yield t}_parse_record(t){throw"NotImplementedError"}},Bg=class extends Lg{NODE_TYPE=5;async _parse_record(t,e,i){let n=(await ep.unpack_from_async("0)throw"Filter info size not supported on FractalHeap";if(e.get("btree_address_huge_objects")!=Vg)throw"Huge objects not implemented in FractalHeap";e.set("btree_address_huge_objects",null),e.get("root_block_address")==Vg&&e.set("root_block_address",null);let i=e.get("log2_maximum_heap_size"),n=this._min_size_nbits(i),r=new Map([["signature","4s"],["version","B"],["heap_header_adddress","Q"],["block_offset",`${n}B`]]);this.indirect_block_header=new Map(r),this.indirect_block_header_size=Xf(r),2==(2&e.get("flags"))&&r.set("checksum","I"),this.direct_block_header=r,this.direct_block_header_size=Xf(r);let s=e.get("maximum_direct_block_size");this._managed_object_offset_size=this._min_size_nbits(i);let o=Math.min(s,e.get("max_managed_object_size"));this._managed_object_length_size=this._min_size_integer(o);let a=e.get("starting_block_size"),l=e.get("table_width");if(!(a>0))throw"Starting block size == 0 not implemented";let h=Number(Math.floor(Math.log2(s)));Qf(1n<0)for await(let t of this._iter_indirect_block(this.fh,f,p))d.push(t);else{let t=await this._read_direct_block(this.fh,f,a);d.push(t)}let g=d.reduce(((t,e)=>t+e.byteLength),0),m=new Uint8Array(g),b=0;d.forEach((t=>{m.set(new Uint8Array(t),b),b+=t.byteLength})),this.managed=m.buffer}async _read_direct_block(t,e,i){let n=await t.slice(e,e+i);return Qf("FHDB"==Yf(this.direct_block_header,n).get("signature")),n}get_data(t){let e=ep.unpack_from(">4&3,n=1;if(0==i){Qf(0==e>>6);let i=this._managed_object_offset_size,r=rp(i,t,n);n+=i,i=this._managed_object_length_size;let s=rp(i,t,n);return this.managed.slice(r,r+s)}throw 1==i?"tiny objectID not supported in FractalHeap":2==i?"huge objectID not supported in FractalHeap":"unknown objectID type in FractalHeap"}_min_size_integer(t){return this._min_size_nbits(np(t))}_min_size_nbits(t){return Math.ceil(t/8)}async*_iter_indirect_block(t,e,i){let n=await Zf(this.indirect_block_header,t,e);e+=this.indirect_block_header_size,Qf("FHIB"==n.get("signature"));let r=n.get("block_offset").reduce(((t,e,i)=>t+(e<<8*i)),0);n.set("block_offset",r);let[s,o]=this._indirect_info(i),a=[];for(let i=0;ithis._chunks))}get shape(){let t=this.find_msg_type(Im)[0].get("offset_to_message");return async function(t,e){let i=(await ep.unpack_from_async("255&&(s=(await ep.unpack_from_async("0;t.set("optional",a);let l,h=(await ep.unpack_from_async("0&&(l=(await ep.unpack_from_async(`${s}s`,i,e))[0],e+=s),t.set("name",l);let c=await ep.unpack_from_async(`<${h}i`,i,e);e+=4*h,t.set("client_data_values",c),r.push(t)}}return this._filter_pipeline=r,this._filter_pipeline}find_msg_type(t){return this.msgs.filter((function(e){return e.get("type")==t}))}async get_attributes(){let t={},e=this.find_msg_type(Fm);for(let i of e){let e=i.get("offset_to_message"),[n,r]=await this.unpack_attribute(e);t[n]=r}return t}async get_fillvalue(){var t,e=this.find_msg_type(Rm)[0].get("offset_to_message");let i=(await ep.unpack_from_async("=r&&([s,r]=a[++l],h=0);let e=await Zf(gm,t,s+h),i=s+h+mm;if(e.set("offset_to_message",i),e.get("type")==Om){var[d,f]=await ep.unpack_from_async("=o-ym){let t=l[++h];if(null==t)break;[r,o]=t,c=0}let e=await Zf(bm,t,r+c),i=r+c+ym+n;if(e.set("offset_to_message",i),e.get("type")==Om){var[u,d]=await ep.unpack_from_async("0,l=(4&n)>0;(8&n)>0?(r=(await ep.unpack_from_async("0&&(e+=8);let r=(2&n)>0?_m:wm,s=await Zf(r,t,e),o=new Map;for(let[t,e]of s.entries())o.set(t,e==nm?null:e);return o}get is_dataset(){return this.find_msg_type(Im).length>0}async get_data(){let t=this.find_msg_type(Bm)[0].get("offset_to_message");var[e,i,n,r]=await this._get_data_message_properties(t);if(0==n)throw"Compact storage of DataObject not implemented";return 1==n?this._get_contiguous_data(r):2==n?this._get_chunked_data(t):void 0}async _get_data_message_properties(t){let e,i,n,[r,s,o]=await ep.unpack_from_async("=1&&r<=4),[r,e,i,n]}async _get_contiguous_data(t){let[e]=await ep.unpack_from_async("=!@\|]?(i|u|f|S)(\d*)/.test(n)){let[t,i,s]=tp(n),a=new Array(r);const l=await this.fh.slice(e,e+s*r);let h=new ip(l);for(var o=0;o=1&&e<=3);var a="<"+(i-1).toFixed()+"I",l=await ep.unpack_from_async(a,this.fh,s);this._chunks=l,this._chunk_dims=i,this._chunk_address=o}}}},nm=ep.unpack_from("this.get(t)))}length(){return this.keys.length}_dereference(t){if(!t)throw"cannot deference null reference";let e=this.file._get_object_by_address(t);if(null==e)throw"reference not found in file";return e}async get(t){if("number"==typeof t)return this._dereference(t);var e=Vm(t);if("/"==e)return this.file;if("."==e)return this;if(/^\//.test(e))return this.file.get(e.slice(1));if(""!=function(t){let e=t.lastIndexOf("/")+1,i=t.slice(0,e),n=new RegExp("^/+$"),r=new RegExp("/$");return i&&!n.test(i)&&(i=i.replace(r,"")),i}(e))var[i,n]=e.split(/\/(.*)/);else var i=e,n=".";if(!(i in this._links))throw i+" not found in group";var r=Vm(this.name+"/"+i);let s=this._links[i];if("string"==typeof s)try{return this.get(s)}catch(t){return null}var o=new im(this.file._fh,s);if(await o.ready,o.is_dataset){if("."!=n)throw r+" is a dataset, not a group";return new Um(r,o,this)}var a=new Pm(r,this);return await a.init(o),a.get(n)}visit(t){return this.visititems(((e,i)=>t(e)))}visititems(t){var e=this.name.length;/\/$/.test(this.name)||(e+=1);for(var i=this.values.slice();i;){let n=i.shift();1==i.length&&console.log(n);let r=t(n.name.slice(e),n);if(null!=r)return r;n instanceof Pm&&(i=i.concat(n.values))}return null}get attrs(){return null==this._attrs&&(this._attrs=this._dataobjects.get_attributes()),this._attrs}},zm=class extends Pm{constructor(t,e,i){super("/",null),this.ready=this.init(t,e,i)}async init(t,e,i){var n=new Fg(t,0);await n.ready;var r=await n.get_offset_to_dataobjects(),s=new im(t,r);if(await s.ready,this.parent=this,this.file=this,this.name="/",this._dataobjects=s,this._attrs=null,this._keys=null,this._fh=t,this.filename=e||"",this.mode="r",this.userblock_size=0,i&&i.index)this.index=i.index;else{let e;if(i&&i.indexOffset)e=i.indexOffset;else{const t=await this.attrs;if(t.hasOwnProperty("_index_offset"))e=t._index_offset;else{const t=this.indexName||"_index",i=await s.find_link(t);i&&(e=i[1])}}if(e)try{const i=new im(t,e);await i.ready;const n=await i.get_data(),r=Ag(n),s=(new TextDecoder).decode(r);this.index=JSON.parse(s)}catch(t){console.error(`Error loading index by offset ${t}`)}}this.index&&this.name in this.index?this._links=this.index[this.name]:this._links=await s.get_links()}_get_object_by_address(t){return this._dataobjects.offset==t?this:this.visititems((t=>{t._dataobjects.offset}))}},Um=class extends Array{constructor(t,e,i){super(),this.parent=i,this.file=i.file,this.name=t,this._dataobjects=e,this._attrs=null,this._astype=null}get value(){var t=this._dataobjects.get_data();return null==this._astype?this.getValue(t):t.astype(this._astype)}get shape(){return this._dataobjects.shape}get attrs(){return this._dataobjects.get_attributes()}get dtype(){return this._dataobjects.dtype}get fillvalue(){return this._dataobjects.get_fillvalue()}async to_array(){return function(t,e){const i=t.length,n=e.reduce(((t,e)=>t*e),1);i!==n&&console.warn(`shape product: ${n} does not match length of flattened array: ${i}`);let r=t;const s=e.slice(1).reverse();for(let t of s){const e=[],{length:i}=r;let n=0;for(;nt.substr(0,t.indexOf("\0")))):t}};function Vm(t){return t.replace(/\/(\/)+/g,"/")}class Hm{constructor(t){this.fileReader=t}async slice(t,e){return this.fileReader.read(t,e-t)}}function jm(t){const e=t.lastIndexOf("/");return e>0?t.substring(e+1):t}class $m{constructor(t,e=1e5){this.h5_file=t,this.bin_size=e,this.h5_obj=void 0}async fetch(){return this.h5_obj||(this.h5_obj=await async function(t){var e;t.url&&"function"==typeof(e=t.url).slice&&"function"==typeof e.arrayBuffer&&(t.file=t.url,t.url=void 0);const i=void 0!==t.url;let n=t.reader?t.reader:function(t){if(t.url)return new $f(t);if(t.path)return new NodeLocalFile(t);if(t.file)return new Gf(t.file);throw Error("One of 'url', 'path (node only)', or 'file (browser only)' must be specified")}(t);const r=t.fetchSize||2e3,s=t.maxSize||2e5;i&&(n=new qf({file:n,fetchSize:r,maxSize:s}));const o=new Hm(n),a=await async function(t){let e;if(t.indexReader)e=t.indexReader;else{if(t.index)return t.index;t.indexURL?e=new $f({url:t.indexURL}):t.indexPath?e=new NodeLocalFile({path:t.indexPath}):t.indexFile&&(e=new Gf({file:t.indexFile}))}if(e){const t=await e.read(),i=(new TextDecoder).decode(t);return JSON.parse(i)}}(t),l=t.indexOffset,h=function(t){return t.url?jm(t.url):t.path?jm(t.path):t.file?t.file.name:void 0}(t),c=new zm(o,h,{index:a,indexOffset:l});return await c.ready,c}({url:this.h5_file,fetchSize:1e6,maxSize:2e8})),this.h5_obj}async get_keys(){return(await this.fetch()).keys}async get_rd_signal(t=this.bin_size){let e=await this.fetch(),i=e.keys,n=new qm(i),r=n.get_rd_bins(),s=n.get_snp_bins();this.available_bins=[...new Set(r,s)],this.available_bins.includes(t)||(t=this.available_bins.at(-1));const o=await e.get("rd_chromosomes");await o.dtype;let a=await o.value,l=await this.rd_stat(e,i,t);var h=[],c=[],u=[],d=[],f=[],p=[];for(let n of a){var g=`his_rd_p_${n}_${t}`;let r=await this.get_chr_signal(e,i,n,t,g,l);h=h.concat(r);var m=`his_rd_p_${n}_${t}_GC`;let s=await this.get_chr_signal(e,i,n,t,m,l);c=c.concat(s);let o=`his_rd_p_${n}_${t}_partition_GC_merge`,a=await this.get_chr_signal(e,i,n,t,o,l);u=u.concat(a);let b=await this.rd_call_combined(e,i,n,t,l);d=d.concat(b);let y=`snp_likelihood_${n}_${t}_mask`,v=await this.get_baf_signals(e,i,n,t,y);f=f.concat(v[0]),p=p.concat(v[1])}this.callers=[],0!=d.length&&this.callers.push("ReadDepth"),0!=d.length&&this.callers.push("2D");var b={},y={RD_Raw:h,RD_Raw_gc_coor:c,ReadDepth:u,"2D":d,BAF1:f,BAF2:p};return b[t]=y,b}decode_segments(t){let e=[],i=[];for(let n of t)4294967295==n?(e.push(i),i=[]):i.push(n);return e}async rd_call_combined(t,e,i,n,r){let s,o=[],a=`his_rd_p_${i}_${n}_partition_GC_mosaic_segments_2d`;if(e.includes(a)){const e=await t.get(a);let i=await e.value;s=this.decode_segments(i)}let l=`his_rd_p_${i}_${n}_partition_GC_mosaic_call_2d`;if(e.includes(l)){const e=await t.get(l);let a=await e.to_array();s.forEach(((t,e)=>{t.forEach(((t,s)=>{o.push({chr:i,start:t*n,end:(t+1)*n,value:a[0][e]/r[4]*2})}))}))}return o}async rd_stat(t,e,i){let n,r=`rd_stat_${i}_auto`;if(e.includes(r)){const e=await t.get(r);n=await e.value}return n}async get_chr_signal(t,e,i,n,r,s){let o=[];if(e.includes(r)){const e=await t.get(r);(await e.value).forEach(((t,e)=>{o.push({chr:i,start:e*n,end:(e+1)*n,value:t/s[4]*2})}))}return o}async get_baf_signals(t,e,i,n,r){let s=[],o=[];if(e.includes(r)){let e=await t.get(r);(await e.to_array()).forEach(((t,e)=>{let r=Math.max(...t);const a=t.indexOf(r);let l=Math.max(a/200,1-a/200);s.push({chr:i,start:e*n,end:(e+1)*n,value:-2*l}),.5!=l&&o.push({chr:i,start:e*n,end:(e+1)*n,value:-2*(1-l)})}))}return[s,o]}async get_baf_signals_v2(t,e,i,n,r){let s=[],o=[];if(e.includes(r)){let e=await t.get(r);(await e.to_array()).forEach(((t,e)=>{isNaN(t)||(s.push({chr:i,start:e*n,end:(e+1)*n,value:-2*(.5-t)}),.5!=t&&o.push({chr:i,start:e*n,end:(e+1)*n,value:-2*(.5+t)}))}))}return console.log(i,s,o),[s,o]}}class qm{constructor(t){this.signals=t}get_rd_bins(){let t=[];return this.signals.forEach((e=>{let i=e.match(/^his_rd_p_(.*)_(\d+)$/);i&&t.push({chr:i[1],bin_size:i[2]})})),[...new Set(t.map((t=>Number(t.bin_size))))]}get_snp_bins(){let t=[];return this.signals.forEach((e=>{let i=e.match(/^snp_likelihood_(.*)_(\d+)_mask$/);i&&t.push({chr:i[1],bin_size:i[2]})})),[...new Set(t.map((t=>Number(t.bin_size))))]}}function Wm(t){let e=function(t){if(t.length<4)return t;let e,i,n,r,s,o;return e=t.slice().sort(((t,e)=>t-e)),e.length/4%1==0?(i=.5*(e[e.length/4]+e[e.length/4+1]),n=.5*(e[e.length*(3/4)]+e[e.length*(3/4)+1])):(i=e[Math.floor(e.length/4+1)],n=e[Math.ceil(e.length*(3/4)+1)]),r=n-i,s=n+1.5*r,o=i-1.5*r,e.filter((t=>t>=o&&t<=s))}(t);const i=e.length,n=e.reduce(((t,e)=>t+e))/i,r=Math.sqrt(e.map((t=>Math.pow(t-n,2))).reduce(((t,e)=>t+e))/i);return[n,r]}var Gm=function(t,e,i){if(void 0===i&&(i=Math.max(Math.round(e-t)+1,1)),i<2)return 1===i?[t]:[];var n=Array(i);for(let r=--i;r>=0;r--)n[r]=(r*e+(i-r)*t)/i;return n},Zm=class{constructor(t){this.allBins=t}getValues(){return Object.values(this.allBins).reduce(((t,e)=>t.concat(e.filter((t=>t.binScore>0)).map((t=>t.binScore)))),[])}getMean(t){return t.reduce((function(t,e){return t+e}))/t.length}fit_data(){return Wm(this.getValues())}histogram(t,e){const i=e[1]-e[0],n=[];t.forEach(((t,r)=>{e.forEach(((e,r)=>{if(n[e]||(n[e]={count:0}),e<=t&&t{r.push(t.count)})),r}};function Ym(t,e){return isNaN(t)||isNaN(e)||e<=0?NaN:0===t?.5:.5+.5*(Qm(.5*e,.5,1)-Qm(.5*e,.5,e/(e+t*t)))*Math.sign(t)}function Qm(t,e,i){if(0==i)return 0;if(1==i)return 1;{let n=tb(t+e)-tb(t)-tb(e)+t*Math.log(i)+e*Math.log(1-i);return i<(t+1)/(t+e+2)?Math.exp(n)*Xm(t,e,i)/t:1-Math.exp(n)*Xm(e,t,1-i)/e}}function Xm(t,e,i,n=1e3){let r=1,s=1,o=1,a=t+e,l=t+1,h=t-1,c=1-a*i/l;for(let u=0;u<=n;u++){let n=parseFloat(u+1),d=n+n,f=n*(e-n)*i/((h+d)*(t+d)),p=r+f*s,g=c+f*o;f=-(t+n)*(a+n)*i/((l+d)*(t+d));let m=g+f*c,b=r;if(s=p/m,o=g/m,r=(p+f*r)/m,c=1,Math.abs(r-b)<3e-7*Math.abs(r))return r}}function Km(t){return 0==t||1==t?1:t*Km(t-1)}function Jm(t){let e;var i=[75122.633153,80916.6278952,36308.2951477,8687.24529705,1168.92649479,83.8676043424,2.50662827511],n=0,r=1;if(0==t)e=1e99;else if(t%1==0)e=Km(t-1);else{for(let e=0;ee?t:e}))}function nb(t,e,i,n){return e*Math.exp(-1*(t-i)**2/(2*n**2))/Math.sqrt(2*Math.PI)/n}function rb(t,e,i,n){return Math.exp(-1*(t-i)**2/(e**2+n**2))}function sb(t,e){let i;try{i=t.reduce(((t,i,n)=>t+Math.min(i,e[n])))}catch{return console.log("Failed to find likelihood overlap: ",t,e),0}return i}function ob(t,e,i,n){return 0==e&&0==n?{nl:.5*(t+i),ne:0}:{nl:(t*n*n+i*e*e)/(e*e+n*n),ne:Math.sqrt(e*e*n*n/(e*e+n*n))}}function ab(t,e){let i=parseInt(e*(t.length-1)),n=e*(t.length-1)-i;return iMath.floor(e/2)&&(n=e-1-n);const r=(e/2-n)/(e+1),s=Math.floor((e/2+n)/2),o=e-1-s;let a=t.slice(s,o+1).reduce(((t,e)=>t+e),0)/t.reduce(((t,e)=>t+e),0);return n===Math.floor(e/2)&&(a=1),{mean:r,p:a}}var hb=class{constructor(t,e){this.wigFeatures=t,this.binSize=e}get_fit(){var t=new Zm(this.wigFeatures),[e,i]=t.fit_data();return{globalMean:e,globalStd:i}}async call_2d(t=null,e=null,i="both",n=.1,r=0,s=10,o=0){let a=this.get_fit();this.globalMean=a.globalMean,this.globalStd=a.globalStd;let l=null==t?.05*this.binSize/3e9:t,h=null==e?parseInt(this.binSize/1e4):e,c=[],u=[],d=[],f=[],p=[],g=[];for(const[t,e]of Object.entries(this.wigFeatures)){let t=[],i=[],s=[];e.forEach(((e,n)=>{e.hets_count>4&&e.dp_count>h&&(t.push([n]),i.push(e.binScore),s.push(e.likelihood_score),delete e.likelihood_score)}));let o=[];for(let t=1;tMath.sqrt(Math.sqrt(t)**2+this.globalStd**2+Math.pow(a[e]/2,2)))),m=[];for(let e=0;e0;){m=m.filter((t=>"number"==typeof t));let e=ib(m);if(isNaN(e)&&console.log("NaN value",m),et*s[o+1][e])),r=n.reduce(((t,e)=>t+e))}catch{console.log(s),console.log("max_overlap:",e,o,m.length),console.log("likelihood: ",o,s[o],s[o+1]),console.log("nlh: ",r)}if(i[o]=a.nl,g[o]=a.ne,s[o]=n.map((function(t){return t/r})),t[o].push(...t[o+1]),i.splice(o+1,1),g.splice(o+1,1),t.splice(o+1,1),s.splice(o+1,1),m.splice(o,1),o0){let t=rb(i[o-1],g[o-1],i[o],g[o])*sb(s[o-1],s[o]);m[o-1]=t}}let b=-1;for(;;){m=[];for(let e=0;et*s[r+1][e])),a=n.reduce(((t,e)=>t+e));s[r]=n.map((function(t){return t/a})),t[r].push(...t[r+1]),t[r]=t[r].sort(((t,e)=>t-e)),i.splice(o,1),g.splice(o,1),t.splice(o,1),s.splice(o,1),o>=t.length&&(r+=1,o=r+1)}else o+=1,o>=t.length&&(r+=1,o=r+1)}if(b==t.length)break;b=t.length}t.forEach(((t,n)=>{let o=lb(s[n]);t.length>1&&(t.forEach(((t,s)=>{u.push(e[t]),o.mean<=r&&c.push(e[t]),e[t].segment_score=i[n]})),d.push(i[n]),f.push(g[n]),p.push(s[n]))}))}let m=parseInt(1e3*(1-o));0==m&&(m=1);let b=Gm(o,1,m),y={},v={};for(let t=10;t>-1;t--)for(let e=0;e1-e+e*t/2)),a=t/2;t>0?(n=.5-e/(e+s),r=b.map(((t,i)=>.5-(1-t+t*e)/(2-2*t+(e+s)*t)))):(n=0,r=b.map(((t,e)=>0*t)));for(let i=0;i{if(!isNaN(r[e])){let n=nb(t*this.globalMean,1,d[i],f[i])*ab(p[i],.5+r[e]);h+=n,n>c&&(c=n,u=b[e])}})),i in y?y[i].push([t,e,s,h/b.length,u]):y[i]=[t,e,s,h/b.length,u]}for(let t=0;tt[3]-e[3]));else if(y[t].sort(((t,e)=>t[3]-e[3])),"both"==i&&(v[t].sort(((t,e)=>t[3]-e[3])),v[t][0][3]>y[t][0][3])){let e=y[t].filter((e=>e[0]!=v[t][0][0]&&e[1]<=v[t][0][1]));y[t]=[v[t][0]].push(...e)}for(let t=0;t{var r={...t};1!=i&&(r.value=t[e]/i*2),n.push(r)}));return n}formatDataStructure_BAF(t,e=2){const i=[],n=[];for(const[e,r]of Object.entries(this.wigFeatures))r.forEach((e=>{var r={...e},s={...e};let o=e[t];.5!=o&&(s.value=-2*(1-o),n.push(s)),r.value=-2*o,i.push(r)}));return[i,n]}};function cb(t){for(var e=1,i=1,n=1*t,r=1;r<50;r++)e*=r,n+=(i*=-1)*Math.pow(t,2*r+1)/(e*(2*r+1));return 2*n/Math.sqrt(3.14159265358979)}function ub(t,e,i,n,r){var s=new pb(i.slice(n,r));return 0==s.std&&(s.std=e>0?e*s.mean/t:1),gb(t,s.mean,s.std,r-n)/(r-n)}function db(t,e,i,n,r){var s=new pb(i.slice(n,r));if(s.means&!h&l0&&(c=ub(t,e,i,n-1,r)),r-n>2)var u=ub(t,e,i,n+1,r),d=ub(t,e,i,n,r-1);if(rt+e))/t.length,this.std=Math.sqrt(t.reduce(((t,e)=>(e-this.mean)**2))/t.length)}}function gb(t,e,i,n){0==i&&(i=1);var r=(t-e)/i*Math.sqrt(n);return 1-eb.TdistributionCDF(Math.abs(r),n-1)}function mb(t,e,i,n,r,s){0==e&&(e=1),0==r&&(r=1);var o=(t-n)/Math.sqrt(e**2/i+r**2/s),a=(e**2/i+r**2/s)**2*(i-1)*(s-1)/(e**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-eb.TdistributionCDF(Math.abs(o),parseInt(a+.5))}var bb=class{constructor(t,e,i){this.rd=t,this.mean=e,this.std=i,this.bin_bands=[2,3,4,5,6,7,8,10,12,14,16,20,24,28,32,40,48,56,64,80,96,112,128]}get_rd_signal_bandwidth(t){var e=[];return t.forEach(((t,i)=>{var n;n=t>this.mean/4?this.mean/(this.std**2*t):4/this.std**2,e.push(n)})),e}meanShiftCaller(t=3){var e={};return Object.entries(this.rd).forEach((([i,n])=>{var r=new Array(n.length).fill(!1),s=new Array(n.length);for(let t=0;t{var o=r.map(((t,e)=>!t)),a=[];Object.entries(n).forEach((([t,e])=>{a.push(e.binScore)}));var l=[0],h=0;for(let t=0;t0&&(l.push(l[l.length-1]+h-1),h=0):h+=1;l.shift();for(let i=0;i=a.length||Math.abs(t-i)>=a.length)){var d=(i-t)*Math.exp(-.5*(i-t)**2/e**2)*Math.exp(-.5*(a[t]-a[i])**2*c[t]);u[t]+=d}for(var f=new Array,p=0;p=0&&f.push(p);f.push(u.length-1),f=f.concat(l).sort(((t,e)=>t-e)),f=Array.from(new Set(f));var g=0;for(p=0;pt+e))/m.length;a.fill(b,g,f[p]+1),g=f[p]+1}}p=0;for(var y=0;p.01&&f.push(p+1);for(f.unshift(0),f.push(s.length),r=new Array(this.rd.length).fill(!1),p=1;p1))continue;w[0]=f[p-2];var _=[f[p],f[p]];if(!(p.01/genome_size*bin_size*(x+k))continue;if(mb(C.mean,C.std,C.data.length,M.mean,M.std,M.data.length)>.01/genome_size*bin_size*(x+S))continue}if(gb(this.mean,C.mean,C.std,C.data.length)>.05)continue;let t=a.slice(v[0],v[1]);var R=new pb(t);r.fill(!0,v[0],v[1]),s.fill(R.mean,v[0],v[1])}})),e[i]=s})),e}call_mean_shift(t=3){for(var e=new Array(this.rd.length).fill(!1),i=new Array(this.rd.length),n=0;n{var s=e.map(((t,e)=>!t)),o=[];s.forEach(((t,e)=>{t&&o.push(this.rd[e])}));for(var a=[0],l=0,h=0;h0&&(a.push(a[a.length-1]+l-1),l=0):l+=1;a.shift();for(var c=0;c=o.length||Math.abs(h-f)>=o.length)){var p=(f-h)*Math.exp(-.5*(f-h)**2/n**2)*Math.exp(-.5*(o[h]-o[f])**2*u[h]);d[h]+=p}var g=new Array;for(h=0;h=0&&g.push(h);g.push(d.length-1),g=g.concat(a).sort(((t,e)=>t-e)),g=Array.from(new Set(g));var m=0;for(h=0;ht+e))/b.length;o.fill(y,m,g[h]+1),m=g[h]+1}}for(h=0,f=0;h.01&&g.push(h+1);for(g.unshift(0),g.push(i.length),e=new Array(this.rd.length).fill(!1),h=1;h1){w[0]=g[h-2];var _=[g[h],g[h]];if(h3.483106931382794e-9*(x+k))continue;if(mb(C.mean,C.std,C.data.length,M.mean,M.std,M.data.length)>3.483106931382794e-9*(x+S))continue}if(!(gb(this.mean,C.mean,C.std,C.data.length)>.05)){var R=new pb(this.rd.slice(v[0],v[1]));e.fill(!0,v[0],v[1]),i.fill(R.mean,v[0],v[1])}}}}}})),i}cnv_calling(t=1e5){var e=(e=.25)*this.mean,i=this.mean-e,n=this.mean+e,r=this.meanShiftCaller(),s={},o=[];return Object.entries(r).forEach((([a,l])=>{for(var h=!1;!h;){h=!0;var c=new Array(1).fill(0);for(let t=0;t.01&&c.push(t+1);c.push(l.length);for(let t=0;t0&&(d=Math.abs(l[c[t]]-l[c[t-1]])),t{g.push(e.binScore)}));for(var m,b=new Array(l.length).fill(""),y=0,v=.05*t/2971e6;y_+1){var x=fb(this.mean,this.std,g,_,k,v);if(x){var k=x;b.fill("D",_,k)}}for(_=y;yn;)y+=1;(k=y)>_+1&&(x=fb(this.mean,this.std,g,_,k,v))&&(k=x,b.fill("A",_,k)),y==w&&(y+=1)}for(y=0;y_+1&&(db(this.mean,this.std,g,_,k)<1682935038707506e-26&&b.fill(["d"]*(k-_),_,k),y-=1),y+=1}(y=0)=b.length););if(y>_){var C=new pb(S.slice(_,y));S.fill(C.mean,_,y)}ya&&(s>0&&e.push({chr:i,start:o,end:a,value:r,bin:l,count:s}),r=0,o=n.start-n.start%this.binSize,a=o+this.binSize);const h=n.calls[9].info.DP;h&&(r+=Number.parseInt(h),s++)}s>0&&e.push({chr:i,start:o,end:a,value:r,bin:l,count:s})}return e}async computeReadDepth(){const t=Object.keys(this.allVariants);var e={};for(let n of t){const t=this.allVariants[n];var i;if(0!==t.length)for(let r of t){i=Math.max(Math.floor(r.start/this.rowBinSize),0),e[n]||(e[n]=[]),e[n][i]||(e[n][i]={chr:n,start:i*this.rowBinSize,end:(i+1)*this.rowBinSize,value:0,sum_score:0,count:0});const t=r.calls[9].info.DP;t&&(e[n][i].sum_score+=Number.parseInt(t),e[n][i].count++)}}var n={};for(let i of t){n[i]||(n[i]=[]);for(let t=0;t{e.forEach(((e,i)=>{e.partition_level=parseInt(s[t][i]),e.partition_call=parseInt(o[0][t][i])}))})),[this.formatDataStructure(t,"binScore",i),this.formatDataStructure(t,"partition_level",i),this.formatDataStructure(t,"partition_call",i),o[1]]}formatDataStructure(t,e,i=1){const n=[];for(const[r,s]of Object.entries(t))s.forEach((t=>{var r={...t};1!=i&&(r.value=t[e]/i*2),n.push(r)}));return n}async computeBAF_v2(){const t=Object.keys(this.allVariants),e={},i=[],n=[];for(let o of t){const t=this.allVariants[o];if(0===t.length)continue;var r;for(let a of t){if(r=Math.max(Math.floor(a.start/this.binSize),0),e[o]||(e[o]=[]),!e[o][r]){if(r>0){let t=r-1;if(e[o][t]){const r=this.get_max_min_score(e[o][t]);if(.5!=r.value){let t=Object.assign({},r);t.value=-2*(1-r.value),n.push(t)}r.value=-2*r.value,e[o][t]=r,i.push(e[o][t])}}e[o][r]={chr:o,start:r*this.binSize,end:(r+1)*this.binSize,value:0,count:0,likelihood_score:[],min_score:0}}const t=a.calls[9];let l=t.genotype,h=t.info.AD.split(","),c=h[0],u=h[1];if(0==l[0]&&1==l[1]||1==l[0]&&0==l[1]){if(0==e[o][r].likelihood_score.length)e[o][r].likelihood_score=Gm(0,1,100).map(((t,e)=>vb(c,u,t)));else{var s=0;e[o][r].likelihood_score=Gm(0,1,100).map(((t,i)=>{var n=e[o][r].likelihood_score[i]*vb(c,u,t);return s+=n,n})),e[o][r].likelihood_score=Gm(0,1,100).map(((t,i)=>e[o][r].likelihood_score[i]/s))}e[o][r].count++}}const a=this.get_max_min_score(e[o][r]);if(.5!=a.value){let t=Object.assign({},a);t.value=-2*(1-a.value),n.push(t)}a.value=-2*a.value,e[o][r]=a,i.push(e[o][r])}return[i,n]}format_BAF_likelihood(t){const e=[];for(const[i,n]of Object.entries(t))n.forEach((t=>{var i={...t};.5!=t.value&&(i.value=1-t.value,e.push(i))}));return e}get_max_min_score(t){if(t.likelihood_score.length>0){const e=Math.max(...t.likelihood_score),i=t.likelihood_score.indexOf(e);t.value=Math.max(i/100,1-i/100),t.min_score=Math.min(i/100,1-i/100)}else t.score=0;return t}async getAllbins(){const t=await this.computeDepthFeatures();return new Zm(t).fit_data(),t}async read_rd_baf(t="ReadDepth"){const e=Object.keys(this.allVariants);var i={};for(let t of e){const e=this.allVariants[t];var n;if(0!==e.length)for(let r of e){n=Math.max(Math.floor(r.start/this.rowBinSize),0),i[t]||(i[t]=[]),i[t][n]||(i[t][n]={chr:t,start:n*this.rowBinSize,end:(n+1)*this.rowBinSize,dp_sum_score:0,dp_count:0,hets_count:0,hets:[]});const e=r.calls[9],s=e.info.DP;s&&(i[t][n].dp_sum_score+=Number.parseInt(s),i[t][n].dp_count++);let o=e.info.AD.split(","),a=e.genotype;if(0==a[0]&&1==a[1]||1==a[0]&&0==a[1]){i[t][n].hets_count++;let e=parseInt(o[0]),r=parseInt(o[1]);i[t][n].hets.push({ref:e,alt:r})}}}var r,s=this.adjust_bin_size(i);if("ReadDepth"==t){r=this.readDepthMeanshift(s);var o=this.formatDataStructure_BAF(s,"max_likelihood")}else if("2D"==t){let t=new hb(s,this.binSize),e=await t.call_2d();r=[e.binScore,[],e.segment_score],o=t.formatDataStructure_BAF("max_likelihood")}return[r,o]}formatDataStructure_BAF(t,e,i=2){const n=[],r=[];for(const[i,s]of Object.entries(t))s.forEach((t=>{delete t.likelihood_score;var i={...t},s={...t};let o=t[e];.5!=o&&(s.value=-2*(1-o),r.push(s)),i.value=-2*o,n.push(i)}));return[n,r]}adjust_bin_size(t){const e=Object.keys(this.allVariants);var i={};for(let s of e){i[s]||(i[s]=[]);for(let e=0;e{if(0==i[s][e].likelihood_score.length)i[s][e].likelihood_score=Gm(0,1,100).map(((e,i)=>vb(t.ref,t.alt,e)));else{var r=0;i[s][e].likelihood_score=Gm(0,1,100).map(((n,o)=>{var a=i[s][e].likelihood_score[o]*vb(t.ref,t.alt,n);return r+=a,a})),i[s][e].likelihood_score=Gm(0,1,100).map(((t,n)=>i[s][e].likelihood_score[n]/r))}}))}const a=this.get_max_min_score(i[s][e]);i[s][e].max_likelihood=a.value}}return i}}function vb(t,e,i,n=!0){return i**t*(1-i)**e+i**e*(1-i)**t}class wb extends ch{constructor(t,e){super(t,e),this.featureType="numeric",this.paintAxis=$u,t.max||(this.defaultScale=!0,this.autoscale=!1),this.height=void 0!==t.height?t.height:250}async init(t){this.type="cnvpytor",this.graphType=t.graphType||"points",this.bin_size=t.bin_size||1e5,this.signal_name=t.signal_name||"rd_snp",this.cnv_caller=t.cnv_caller||"2D",this.colors=t.colors||["gray","black","green","blue"],super.init(t)}get supportsWholeGenome(){return!0}get_signals(){let t=[];return"rd_snp"==this.signal_name?t=["RD_Raw","RD_Raw_gc_coor",this.cnv_caller,"BAF1","BAF2"]:"rd"==this.signal_name?t=["RD_Raw","RD_Raw_gc_coor",this.cnv_caller]:"snp"==this.signal_name?t=["BAF1","BAF2"]:"cnh"==this.signal_name&&(t=[this.cnv_caller]),t}get_signal_colors(){return[{singal_name:"RD_Raw",color:this.colors[0]},{singal_name:"RD_Raw_gc_coor",color:this.colors[1]},{singal_name:"ReadDepth",color:this.colors[2]},{singal_name:"2D",color:this.colors[2]},{singal_name:"BAF1",color:this.colors[3]},{singal_name:"BAF2",color:this.colors[3]}]}async postInit(){if("vcf"==this.config.format){this.featureSource=$c(this.config,this.browser.genome),this.header=await this.getHeader();var t=this.featureSource.reader.features.reduce((function(t,e){return t[e.chr]=t[e.chr]||[],t[e.chr].push(e),t}),Object.create(null));const e=new yb(t,this.bin_size);let i,n,r;this.wigFeatures_obj={},this.wigFeatures_obj[this.bin_size]={},"2D"==this.config.cnv_caller?(r=await e.read_rd_baf("2D"),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size]["2D"]=i[2],this.available_callers=["2D"]):(r=await e.read_rd_baf(),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size].ReadDepth=i[2],this.available_callers=["ReadDepth"]),this.wigFeatures_obj[this.bin_size].RD_Raw=i[0],this.wigFeatures_obj[this.bin_size].RD_Raw_gc_coor=i[1],this.wigFeatures_obj[this.bin_size].BAF1=n[0],this.wigFeatures_obj[this.bin_size].BAF2=n[1],this.available_bins=[this.bin_size],this.set_available_callers()}else this.cnvpytor_obj=new $m(this.config.url,this.bin_size),this.wigFeatures_obj=await this.cnvpytor_obj.get_rd_signal(this.bin_size),this.available_bins=this.cnvpytor_obj.available_bins,this.available_callers=this.cnvpytor_obj.callers,this.set_available_callers();this.tracks=[];const e=[];this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(let t in this.wigFeatures_obj)for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:"wig",isMergedTrack:!0};t.features=n,t.name=i,t.color=this.signal_colors.filter((t=>t.singal_name===i)).map((t=>t.color));const r=await this.browser.createTrack(t);r?(r.autoscale=!1,this.tracks.push(r)):console.warn("Could not create track "+t),"function"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return Promise.all(e)}set_available_callers(){this.available_callers.includes(this.cnv_caller)||(this.available_callers.length>0?this.cnv_caller=this.available_callers[0]:this.cnv_caller=null)}async getHeader(){if(!this.header){if("function"==typeof this.featureSource.getHeader){const t=await this.featureSource.getHeader();t&&(this.callSets=t.callSets||[]),this.header=t}this.sampleNames=this.callSets?this.callSets.map((t=>t.name)):[]}return this.header}get height(){return this._height}set height(t){if(this._height=t,this.tracks)for(let e of this.tracks)e.height=t,e.config.height=t}menuItemList(){let t=[];void 0!==this.flipAxis&&t.push({label:"Flip y-axis",click:()=>{this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),t=t.concat(Ui.numericDataMenuItems(this.trackView)),t.push("
"),t.push("Bin Sizes");for(let e of this.available_bins){const i=zi(e,e===this.bin_size);t.push({object:fe(i),click:async()=>{this.bin_size=e,await this.recreate_tracks(e),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}t.push("
"),t.push("Signal Type");let e={rd_snp:"RD and BAF Likelihood",rd:"RD Signal",snp:"BAF Likelihood"};for(let i in e){const n=zi(e[i],i===this.signal_name);t.push({object:fe(n),click:async()=>{this.signal_name=i,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}t.push("
"),t.push("CNV caller");for(let e of this.available_callers){const i=zi(e,e===this.cnv_caller);t.push({object:fe(i),click:async()=>{this.cnv_caller=e,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}return t}async recreate_tracks(t){this.tracks=[];const e=[];t in this.wigFeatures_obj||(this.wigFeatures_obj={...this.wigFeatures_obj,...await this.cnvpytor_obj.get_rd_signal(t)}),this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:"wig",isMergedTrack:!0};t.features=n,t.name=i,t.color=this.signal_colors.filter((t=>t.singal_name===i)).map((t=>t.color));const r=await this.browser.createTrack(t);r?(r.autoscale=!1,this.tracks.push(r)):console.warn("Could not create track "+t),"function"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let t of this.tracks)t.autoscale=!1,t.dataRange=this.dataRange;return Promise.all(e)}async getFeatures(t,e,i,n){if(this.tracks){const r=this.tracks.map((r=>r.getFeatures(t,e,i,n)));return Promise.all(r)}}getScaleFactor(t,e,i,n){return n?i/(Math.log10(e+1)-(t<=0?0:Math.log10(t+1))):i/(e-t)}computeYPixelValue(t,e){return(this.flipAxis?t-this.dataRange.min:this.dataRange.max-t)*e}computeYPixelValueInLogScale(t,e){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),t=Math.log10(t+1),(this.flipAxis?t-n:i-t)*e)}draw(t){const e=t.features;if(!e)return;if(this.defaultScale&&("rd_snp"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||-2,max:this.config.max||this.dataRange.max||6}:"rd"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||0,max:this.config.max||this.dataRange.max||6}:"snp"==this.signal_name&&(this.dataRange={min:this.config.min||this.dataRange.min||-2,max:this.config.max||this.dataRange.max||0})),this.autoscale&&(this.dataRange=function(t,e){let i=0,n=-Number.MAX_VALUE;for(let t of e)for(let e of t)void 0===e.value||Number.isNaN(e.value)||(i=Math.min(i,e.value),n=Math.max(n,e.value));return{min:i,max:n}}(t.referenceFrame.chr,e)),this.tracks)for(let i=0,n=this.tracks.length;ithis.logScale?this.computeYPixelValueInLogScale(t,i):this.computeYPixelValue(t,i);if(this.config.hasOwnProperty("guideLines"))for(let e of this.config.guideLines)if(e.hasOwnProperty("color")&&e.hasOwnProperty("y")&&e.hasOwnProperty("dotted")){let i=n(e.y),r={strokeStyle:e.color,strokeWidth:1};e.dotted?na.dashedLine(t.context,0,i,t.pixelWidth,i,5,r):na.strokeLine(t.context,0,i,t.pixelWidth,i,r)}}popupData(t,e){const i=e||t.viewport.cachedFeatures;if(i&&i.length===this.tracks.length){const e=[];for(let n=0;n0&&e.push("
"),e.push(`
${this.tracks[n].name}
`);const r=this.tracks[n].popupData(t,i[n]);e.push(...r)}return e}}}const _b=new Map([["ideogram",(t,e)=>new zf(t,e)],["sequence",(t,e)=>new Xa(t,e)],["feature",(t,e)=>new Nd(t,e)],["seg",(t,e)=>new gf(t,e)],["mut",(t,e)=>new gf(t,e)],["maf",(t,e)=>new gf(t,e)],["wig",(t,e)=>new uf(t,e)],["merged",(t,e)=>new bf(t,e)],["alignment",(t,e)=>new jd(t,e)],["interaction",(t,e)=>new vf(t,e)],["interact",(t,e)=>new vf(t,e)],["variant",(t,e)=>new If(t,e)],["eqtl",(t,e)=>new Mf(t,e)],["gwas",(t,e)=>new Bf(t,e)],["arc",(t,e)=>new Of(t,e)],["gcnv",(t,e)=>new Nf(t,e)],["junction",(t,e)=>new jf(t,e)],["blat",(t,e)=>new Ud(t,e)],["cnvpytor",(t,e)=>new wb(t,e)]]);var xb=function(t,e){_b.set(t,e)};class kb{constructor(t,e){const i=(new DOMParser).parseFromString(t,"text/xml");this.processRootNode(i,e);const n=i.getElementsByTagName("Resource"),r=i.getElementsByTagName("Track"),s=r&&r.length>0,o=[];this.tracks=o;const a=new Map;Array.from(n).forEach((function(t,e){var i={url:t.getAttribute("path"),indexURL:t.getAttribute("index"),order:e};a.set(i.url,i),s||o.push(i)})),s&&Array.from(r).forEach((function(t){const e=t.getElementsByTagName("Track");if(e&&e.length>0){const i={type:"merged",tracks:[]};Sb(t,i),o.push(i),Array.from(e).forEach((function(t){t.processed=!0;const e=t.getAttribute("id"),n=a.get(e);n&&(i.tracks.push(n),Sb(t,n),n.autoscale=!1,i.height=n.height)}))}else if(!t.processed){const e=t.getAttribute("id"),i=a.get(e);i&&(o.push(i),Sb(t,i))}}))}processRootNode(t,e){const i=t.getElementsByTagName("Session");!i||i.length;const n=i.item(0),r=n.getAttribute("genome"),s=n.getAttribute("locus"),o=n.getAttribute("ucscID");e&&e.hasOwnProperty(r)?this.genome=r:(this.reference={fastaURL:r},o&&(this.reference.id=o)),s&&(this.locus=s)}}function Sb(t,e){e.name=t.getAttribute("name");const i=t.getAttribute("color");i&&(e.color="rgb("+i+")");const n=t.getAttribute("altColor");i&&(e.altColor="rgb("+n+")");const r=t.getAttribute("height");r&&(e.height=parseInt(r));const s=t.getAttribute("autoScale");s&&(e.autoscale="true"===s);const o=t.getAttribute("autoscaleGroup");o&&(e.autoscaleGroup=o);const a=t.getAttribute("windowFunction");a&&(e.windowFunction=a);const l=t.getAttribute("visibilityWindow")||t.getAttribute("featureVisibilityWindow");l&&(e.visibilityWindow=l);const h=t.getAttribute("indexed");h&&(e.indexed="true"===h);const c=t.getAttribute("normalize");c&&(e.normalize="true"===c);const u=t.getElementsByTagName("DataRange");if(u.length>0){const t=u.item(0);e.min=Number(t.getAttribute("minimum")),e.max=Number(t.getAttribute("maximum")),e.logScale="LOG"===t.getAttribute("type")}}const Cb=qi;class Ab{constructor(){this.attributes={},this.plinkLoaded=!1}async loadPlinkFile(t,e){e||(e={});var i=la(e);const n=await zo.loadString(t,i);var r=Cb(n);for(let t of r){var s=t.split(" ");this.attributes[s[1]]={familyId:s[0],fatherId:s[2],motherId:s[3],sex:s[4],phenotype:s[5]}}return this.plinkLoaded=!0,this}getAttributes(t){return this.attributes[t]}getAttributeNames(){return this.hasAttributes()?Object.keys(this.attributes[Object.keys(this.attributes)[0]]):[]}hasAttributes(){return Object.keys(this.attributes).length>0}}class Tb{constructor(t,e){this.geneColors={},this.gene=null,this.snp=null,this.genesCount=0,t&&(this.gene=t.toUpperCase(),this.geneColors[this.gene]=Ib[this.genesCount++]),e&&(this.snp=e.toUpperCase())}addGene(t){this.geneColors[t.toUpperCase()]||(this.geneColors[t.toUpperCase()]=Ib[this.genesCount++])}colorForGene(t){return this.geneColors[t.toUpperCase()]}}var Ib=[];Ib.push("rgb(228,26,28)"),Ib.push("rgb(55,126,184)"),Ib.push("rgb(77,175,74)"),Ib.push("rgb(166,86,40)"),Ib.push("rgb(152,78,163)"),Ib.push("rgb(255,127,0)"),Ib.push("rgb(247,129,191)"),Ib.push("rgb(153,153,153)"),Ib.push("rgb(255,255,51)"),Ib.push("rgb(102, 194, 165"),Ib.push("rgb(252, 141, 98"),Ib.push("rgb(141, 160, 203"),Ib.push("rgb(231, 138, 195"),Ib.push("rgb(166, 216, 84"),Ib.push("rgb(255, 217, 47"),Ib.push("rgb(229, 196, 148"),Ib.push("rgb(179, 179, 179"),Ib.push("rgb( 141, 211, 199"),Ib.push("rgb(255, 255, 179"),Ib.push("rgb(190, 186, 218"),Ib.push("rgb(251, 128, 114"),Ib.push("rgb(128, 177, 211"),Ib.push("rgb(253, 180, 98"),Ib.push("rgb(179, 222, 105"),Ib.push("rgb(252, 205, 229"),Ib.push("rgb(217, 217, 217"),Ib.push("rgb(188, 128, 189"),Ib.push("rgb(204, 235, 197"),Ib.push("rgb(255, 237, 111");class Eb{constructor(t,e,i,n,r){this.genome=t,this.chr=e,this.start=i,this.end=n,this.bpPerPixel=r,this.id=_e.guid()}extend(t){const e=Math.min(t.start,this.start),i=Math.max(t.end,this.end),n=(i-e)/(this.end-this.start);this.start=e,this.end=i,this.bpPerPixel*=n}calculateEnd(t){return this.start+this.bpPerPixel*t}calculateBPP(t,e){return(t-this.start)/e}set(t){this.chr=t.chr,this.start=t.start,this.bpPerPixel=t.bpPerPixel}toPixels(t){return t/this.bpPerPixel}toBP(t){return this.bpPerPixel*t}shiftPixels(t,e,i){const n=this.start,r=t*this.bpPerPixel;return this.start+=r,i&&this.clampStart(e),this.end=this.start+e*this.bpPerPixel,n!==this.start}clampStart(t){const e=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(e,this.start),t){const{bpLength:e}=this.genome.getChromosome(this.chr),i=e-t*this.bpPerPixel;this.start>i&&(this.start=i)}}async zoomWithScaleFactor(t,e,i,n){const r=void 0===n?this.start+this.toBP(i/2):n,{start:s,bpPerPixel:o}=this.start,{bpLength:a}=this.getChromosome(),l=e<1?t.minimumBases()/i:a/i;this.bpPerPixel=e<1?Math.max(this.bpPerPixel*e,l):Math.min(this.bpPerPixel*e,l);const h=this.bpPerPixel*i;this.start=r-.5*h,this.clampStart(i),this.end=this.start+h,(s!==this.start||o!==this.bpPerPixel)&&await t.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabelBPLengthOnly(t){const e=" ",i=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*t);return`${e}${this.chr}${e}${da(n-i)}${e}`}getMultiLocusLabelLocusOnly(t){const e=" ",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(t);return`${e}${i}:${n}-${r}${e}`}getMultiLocusLabel(t){const e=" ",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(t),s=Math.floor(this.start)+1;return`${e}${i}:${n}-${r}${e}${e}(${da(Math.round(this.start+this.bpPerPixel*t)-s)})${e}`}getPresentationLocusComponents(t){if("all"===this.chr)return{chr:this.chr};{const e=$i(Math.floor(this.start)+1),i=$i(Math.round(this.start+this.bpPerPixel*t));return{chr:this.chr,start:e,end:i}}}getLocusString(){if("all"===this.chr)return"all";{const t=$i(Math.floor(this.start)+1),e=$i(Math.round(this.end));return`${this.chr}:${t}-${e}`}}description(t){console.log(` ${t||""} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${$i(Math.round(this.start))} end ${$i(Math.round(this.end))} `)}}const Mb={timeout:5e3,type:"plain",url:"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$",coords:0,chromosomeField:"chromosome",startField:"start",endField:"end",geneField:"gene",snpField:"snp"};class Rb{constructor(t){this.browser=t}navbarDidResize(t){this.updateNavbar(this.createResponsiveClassSchedule(t))}updateNavbar(t){this.browser.$toggle_button_container.removeClass(),this.browser.$toggle_button_container.addClass(t.$toggle_button_container),fe(this.browser.zoomWidget.zoomContainer).removeClass(),fe(this.browser.zoomWidget.zoomContainer).addClass(t.zoomContainer)}createResponsiveClassSchedule(t){let e={};const i=this.browser.isMultiLocusWholeGenomeView()||this.browser.referenceFrameList&&ul.isWholeGenomeView(this.browser.referenceFrameList[0].chr);return i?this.browser.windowSizePanel.hide():this.browser.windowSizePanel.show(),t>990?(e.$toggle_button_container="igv-navbar-toggle-button-container",e.zoomContainer="igv-zoom-widget"):t>860?(e.$toggle_button_container="igv-navbar-toggle-button-container",e.zoomContainer="igv-zoom-widget-900"):t>540?(e.$toggle_button_container="igv-navbar-toggle-button-container-750",e.zoomContainer="igv-zoom-widget-900"):(e.$toggle_button_container="igv-navbar-toggle-button-container-750",e.zoomContainer="igv-zoom-widget-900",this.browser.windowSizePanel.hide()),i&&(e.zoomContainer="igv-zoom-widget-hidden"),e}}const Lb=function(t,e){this.container=_e.div({class:"igv-chromosome-select-widget-container"}),e.appendChild(this.container),this.select=document.createElement("select"),this.select.setAttribute("name","chromosome-select-widget"),this.container.appendChild(this.select),this.select.addEventListener("change",(()=>{this.select.blur(),""!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes};Lb.prototype.show=function(){this.container.style.display="flex"},Lb.prototype.hide=function(){this.container.style.display="none"},Lb.prototype.update=function(t){const e=this.showAllChromosomes?t.chromosomeNames.slice():t.wgChromosomeNames.slice();t.showWholeGenomeView()&&(e.unshift("all"),e.unshift("")),this.select.innerHTML="";for(let t of e){const e=document.createElement("option");e.setAttribute("value",t),e.innerText=t,this.select.appendChild(e)}};class Bb{constructor(t,e){this.container=_e.div({class:"igv-windowsize-panel-container"}),t.appendChild(this.container),e.on("locuschange",(t=>{this.updatePanel(t)})),this.browser=e}show(){this.container.style.display="block"}hide(){this.container.style.display="none"}updatePanel(t){const e=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===t.length?da(Math.round(e*t[0].bpPerPixel)):""}}class Nb{constructor(t,e){this.browser=e,this.columnContainer=t,this.horizontalGuide=_e.div({class:"igv-cursor-guide-horizontal"}),t.appendChild(this.horizontalGuide),this.verticalGuide=_e.div({class:"igv-cursor-guide-vertical"}),t.appendChild(this.verticalGuide),this.addMouseHandler(e),this.setVisibility(e.config.showCursorGuide)}addMouseHandler(t){this.boundMouseMoveHandler=function(e){const{x:i,y:n}=_e.translateMouseCoordinates(e,this.columnContainer);this.horizontalGuide.style.top=`${n}px`;const r=function(t,e){for(;t.parentElement;){if(t.parentElement.classList.contains("igv-viewport"))return t.parentElement;t=t.parentElement}}(document.elementFromPoint(e.clientX,e.clientY));if(r&&t.getRulerTrackView()){this.verticalGuide.style.left=`${i}px`;const n=t.root.querySelectorAll(".igv-column");let s;const o=r.parentElement;for(let t=0;t{t.cursorGuideVisible=!t.cursorGuideVisible,t.setCursorGuideVisibility(t.cursorGuideVisible),this.setButtonState(t.cursorGuideVisible)})),this.setButtonState(t.cursorGuideVisible),t.config.showCursorTrackingGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setButtonState(this.browser.cursorGuideVisible)}hide(){this.button.style.display="none"}}class Ob{constructor(t,e){this.browser=t,this.button=_e.div({class:"igv-navbar-button"}),e.appendChild(this.button),this.button.textContent="center line",this.button.addEventListener("click",(()=>{t.isCenterLineVisible=!t.isCenterLineVisible,t.setCenterLineVisibility(t.isCenterLineVisible),this.setButtonState(t.isCenterLineVisible)})),this.setButtonState(t.isCenterLineVisible),t.config.showCenterGuideButton?this.show():this.hide()}setButtonState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.isVisible=!0,this.button.style.display="block",this.setButtonState(this.browser.isCenterLineVisible)}hide(){this.isVisible=!1,this.button.style.display="none"}}class Db{constructor(t,e){this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="track labels",this.button.addEventListener("click",(()=>{e.trackLabelsVisible=!e.trackLabelsVisible,this.setState(e.trackLabelsVisible),e.setTrackLabelVisibility(e.trackLabelsVisible)})),this.browser=e,this.setVisibility(e.config.showTrackLabelButton),this.setState(e.trackLabelsVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.trackLabelsVisible)}hide(){this.button.style.display="none"}}class Pb{constructor(t,e){this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.innerText="Sample Names",this.setState(e.showSampleNames),this.setVisibility(e.showSampleNameButton),this.button.addEventListener("click",(()=>{e.showSampleNames=!e.showSampleNames,this.setState(e.showSampleNames);for(let{sampleNameViewport:t}of e.trackViews)!1===e.showSampleNames?t.hide():t.show();e.layoutChange()}))}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}hide(){this.button.style.display="none"}show(){this.button.style.display="block"}}let zb=23,Ub=0;const Vb=function(t,e){this.browser=t,this.zoomContainer=_e.div({class:"igv-zoom-widget"}),e.appendChild(this.zoomContainer),this.zoomOutButton=_e.div(),this.zoomContainer.appendChild(this.zoomOutButton),this.zoomOutButton.appendChild(_i.createIcon("minus-circle")),this.zoomOutButton.addEventListener("click",(()=>{t.zoomOut()}));const i=_e.div();this.zoomContainer.appendChild(i),this.slider=document.createElement("input"),this.slider.type="range",this.slider.min="0",this.slider.max=`${zb}`,i.appendChild(this.slider),this.slider.addEventListener("change",(e=>{e.preventDefault(),e.stopPropagation();const i=t.referenceFrameList[0],{bpLength:n}=i.genome.getChromosome(i.chr),{end:r,start:s}=i,o=r-s,a=n/Math.pow(2,e.target.valueAsNumber);t.zoomWithScaleFactor(a/o)})),this.zoomInButton=_e.div(),this.zoomContainer.appendChild(this.zoomInButton),this.zoomInButton.appendChild(_i.createIcon("plus-circle")),this.zoomInButton.addEventListener("click",(()=>{t.zoomIn()})),t.on("locuschange",(t=>{this.browser.isMultiLocusMode()?this.disable():(this.enable(),this.update(t))}))};Vb.prototype.update=function(t){const e=t[0],{bpLength:i}=e.genome.getChromosome(e.chr),{start:n,end:r}=e;zb=Math.ceil(Math.log2(i/this.browser.minimumBases())),this.slider.max=`${zb}`;const s=i/(r-n);Ub=Math.log2(s),this.slider.value=`${Math.round(Ub)}`},Vb.prototype.enable=function(){this.slider.disabled=!1},Vb.prototype.disable=function(){this.slider.disabled=!0},Vb.prototype.hide=function(){this.zoomContainer.style.display="none"},Vb.prototype.show=function(){this.zoomContainer.style.display="block"},Vb.prototype.hideSlider=function(){this.slider.style.display="none"},Vb.prototype.showSlider=function(){this.slider.style.display="block"};const Hb=function(t,e){const i=_e.div({class:"igv-navbar-button"});t.append(i),i.textContent="Save SVG",i.addEventListener("click",(()=>e.saveSVGtoFile({})))};class jb{constructor(t,e,i){this.browser=t,this.referenceFrame=e,this.column=i,this.container=_e.div({class:"igv-center-line"}),i.appendChild(this.container),t.isCenterLineVisible?this.show():this.hide()}repaint(){if(this.referenceFrame)if(1/this.referenceFrame.bpPerPixel>1){const t=Math.floor(this.referenceFrame.toPixels(1));this.container.style.width=`${t}px`,this.container.classList.remove("igv-center-line-thin"),this.container.classList.add("igv-center-line-wide")}else this.container.style.width="1px",this.container.classList.remove("igv-center-line-wide"),this.container.classList.add("igv-center-line-thin")}show(){this.isVisible=!0,this.container.style.display="block",this.repaint()}hide(){this.isVisible=!1,this.container.style.display="none"}resize(){this.repaint()}}const $b=$i;class qb{constructor(t){this.browser=t,this.height=40,this.name="",this.id="ruler",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type="ruler"}async getFeatures(t,e,i){return[]}computePixelHeight(t){return this.height}draw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n,bpPerPixel:r,bpStart:s}){ul.isWholeGenomeView(e.chr)?this.drawWholeGenome({context:t,pixelWidth:i,pixelHeight:n,bpPerPixel:r}):this.doDraw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n,bpStart:s})}drawWholeGenome({context:t,pixelWidth:e,pixelHeight:i,bpPerPixel:n}){t.save(),na.fillRect(t,0,0,e,i,{fillStyle:"white"});for(let e of this.browser.genome.wgChromosomeNames){let r=this.browser.genome.getCumulativeOffset(e),s=this.browser.genome.getChromosome(e).bpLength,o=Math.round(r/n),a=Math.round(s/n);this.renderChromosomeRect(t,o,0,a,i,e)}t.restore()}doDraw({context:t,referenceFrame:e,pixelWidth:i,pixelHeight:n,bpStart:r}){t.clearRect(0,0,i,n);const s=function(t,e){if(t<10)return new Wb(1,"bp",1);const i=Math.floor(Math.log10(t));let n="bp",r=1;i>9?(n="gb",r=1e9):i>6?(n="mb",r=1e6):i>3&&(n="kb",r=1e3);const s=t/Math.pow(10,i-1),o=Math.pow(10,i-1),a=Math.pow(10,i)/2;return new Wb(s<75&&!0!==e?o:a,n,r)}(Math.floor(e.toBP(i)),t.isSVG);let o=Math.floor(r/s.majorTick)-1;const{tickDelta:a,labelLength:l}=function(t,e,i,n,r){const s=l(e,a(1+n,r),i)-l(e,a(n,r),i),o=`${$i(Math.floor(a(n,r)/r.unitMultiplier))} ${r.majorUnit}`;return{tickDelta:s,labelLength:Math.floor(t.measureText(o).width)};function a(t,e){return Math.floor(t*e.majorTick)}function l(t,e,i){return Math.round(t.toPixels(e-1-i+.5))}}(t,e,r,o,s);let h,c;this.browser.referenceFrameList.indexOf(e);let u=a;const d=.25*l;do{c=Math.floor(o*s.majorTick);const i=`${$i(Math.floor(c/s.unitMultiplier))} ${s.majorUnit}`;h=Math.round(e.toPixels(c-1-r+.5));const n=Math.round(h-t.measureText(i).width/2);n>0&&d+l<=u&&(na.fillText(t,i,n,this.height-8),u=0),h>0&&na.strokeLine(t,h,this.height-6,h,this.height-2),c=Math.floor((1+o)*s.majorTick);let f=h+(Math.round(e.toPixels(c-1-r+.5))-h)/2;f>0&&na.strokeLine(t,f,this.height-6,f,this.height-2),++o,u+=a}while(ht.measureText(o).width&&na.fillText(t,o,e+n/2,i+r/2,{fillStyle:xo.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Wb{constructor(t,e,i){this.majorTick=t,this.minorTick=t/10,this.majorUnit=e,this.unitMultiplier=i}description(t){console.log((t||"")+" tick "+$b(this.majorTick)+" label width "+$b(this.labelWidthBP)+" multiplier "+this.unitMultiplier)}}const Gb=function(t,e){this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="circular view",this.button.addEventListener("click",(()=>{e.circularViewVisible=!e.circularViewVisible})),this.browser=e,this.setVisibility(e.config.showCircularViewButton),this.setState(e.circularViewVisible)};Gb.prototype.setVisibility=function(t){!0===t?this.show():this.hide()},Gb.prototype.setState=function(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")},Gb.prototype.show=function(){this.button.style.display="block",this.setState(this.browser.circularViewVisible)},Gb.prototype.hide=function(){this.button.style.display="none"};const Zb=function(t,e,i){const n=_e.div({class:"igv-navbar-button"});t.append(n),n.textContent=i.label,n.addEventListener("click",(()=>i.callback(e)))};class Yb{constructor(t,e,i,n,r){this.browser=t,this.roiMenu=e,this.roiTable=i,this.top=n,this.roiSets=r||[],this.boundLocusChangeHandler=Qb.bind(this),t.on("locuschange",this.boundLocusChangeHandler)}async initialize(){this.roiSets.length>0&&(this.browser.showROITableButton=!0,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton));const t=this.roiSets.map((t=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})));t.length>0&&await Promise.all(t);const e=await this.getTableRecords();this.roiTable.renderTable(e)}async loadROI(t,e){const i=Array.isArray(t)?t:[t];for(let t of i)this.roiSets.push(new Gc(t,e));await this.initialize()}clearROIs(){this.roiTable.clearTable();const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();for(let t of this.roiSets)t.dispose();this.roiSets=[]}async getTableRecords(){const t=[];for(let e of this.roiSets){const i=e.isUserDefined?"":e.name||"",n=await e.getAllFeatures();for(let e of Object.keys(n))for(let r of n[e])t.push({setName:i,feature:r})}return t}presentTable(){this.roiTable.present()}async repaintTable(){const t=await this.getTableRecords();this.roiTable.renderTable(t)}dismissTable(){this.roiTable.dismiss()}async updateUserDefinedROISet(t){let e=await this.getUserDefinedROISet();void 0===e&&(e=this.initializeUserDefinedROISet()),e.addFeature(t),!1===this.browser.showROITableButton&&this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e});const i=await this.getTableRecords();this.roiTable.renderTable(i)}setROITableButtonVisibility(t){this.browser.showROITableButton=t,this.browser.roiTableControl.setVisibility(this.browser.showROITableButton)}async renderAllROISets(){for(let t of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t})}async renderROISet({browser:t,pixelTop:e,roiSet:i}){const n=t.columnContainer.querySelectorAll(".igv-column");for(let r=0;ra)&&t.remove()}const c=await i.getFeatures(s,o,a);if(c)for(let h of c){const c=Xb(s,h.start,h.end),{x:u,width:d}=Zc(Math.max(o,h.start),Math.min(a,h.end),o,l),f=n[r].querySelector(Kb(c));if(f)f.style.left=`${u}px`,f.style.width=`${d}px`;else{const s=this.createRegionElement(t.columnContainer,e,u,d,i,c,h.name);n[r].appendChild(s)}}}}createRegionElement(t,e,i,n,r,s,o){const a=_e.div({class:"igv-roi-region"});a.style.top=`${e}px`,a.style.left=`${i}px`,a.style.width=`${n}px`,a.style.backgroundColor=r.color,a.dataset.region=s;const l=_e.div();return a.appendChild(l),l.style.backgroundColor=r.headerColor,!0===r.isUserDefined?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation();const{x:i,y:n}=_e.translateMouseCoordinates(e,t);this.roiMenu.present(i,n,this,t,a)})):o?l.addEventListener("click",(e=>{e.preventDefault(),e.stopPropagation(),this.popover&&this.popover.dispose(),this.popover=new Oi(t,r.name),this.popover.presentContentWithEvent(e,o)})):l.style.pointerEvents="none",a}renderSVGContext(t,{deltaX:e,deltaY:i}){for(const n of document.querySelectorAll(".igv-roi-region")){const{x:r,y:s,width:o,height:a}=n.getBoundingClientRect();t.fillStyle=n.style.backgroundColor,t.fillRect(r+e,s+i,o,a);const l=n.querySelector("div"),{x:h,y:c,width:u,height:d}=l.getBoundingClientRect();t.fillStyle=l.style.backgroundColor,t.fillRect(h+e,c+i,u,d)}}async getUserDefinedROISet(){return this.roiSets.find((t=>!0===t.isUserDefined))}initializeUserDefinedROISet(){const t=new Gc({isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(t),t}async deleteUserDefinedRegionWithKey(t,e){e.querySelectorAll(Kb(t)).forEach((t=>t.remove()));const i=await this.findUserDefinedRegionWithKey(t),n=await this.getUserDefinedROISet();n&&n.removeFeature(i),0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}async findUserDefinedRegionWithKey(t){const{chr:e,start:i,end:n}=Jb(t),r=await this.getUserDefinedROISet();if(r){const t=await r.getFeatures(e,i,n);for(let r of t)if(r.chr===e&&r.start>=i&&r.end<=n)return r}}toJSON(){return this.roiSets.map((t=>t.toJSON()))}dispose(){this.browser.off("locuschange",this.boundLocusChangeHandler);const t=this.browser.columnContainer.querySelectorAll(".igv-roi-region");for(let e of t)e.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let t of this.roiSets)t.dispose();for(let t of Object.keys(this))this[t]=void 0}}function Qb(){this.renderAllROISets()}function Xb(t,e,i){return`${t}-${e}-${i}`}function Kb(t){return`[data-region="${t}"]`}function Jb(t){let[e,i,n]=t.split("-");return i=parseInt(i),n=parseInt(n),{chr:e,start:i,end:n,locus:`${e}:${i}-${n}`,bedRecord:`${e}\t${i}\t${n}`}}class ty extends Fd{constructor(t){super(Object.assign({width:"512px"},t))}tableRowDOM(t){const e=_e.div({class:"igv-roi-table-row"}),{setName:i,feature:n}=t;e.dataset.region=Xb(n.chr,n.start,n.end);let r=[n.chr,$i(n.start),$i(n.end),n.name||"",i];4===this.columnFormat.length&&(r=r.slice(0,4));for(let t=0;tt.remove())),t.length>0){const e=t.sort(((t,e)=>t.feature.chr.localeCompare(e.feature.chr)||t.feature.start-e.feature.start||t.feature.end-e.feature.end));for(let t of e){const e=this.tableRowDOM(t);this.tableRowContainer.appendChild(e)}}}dispose(){document.removeEventListener("click",this.boundGotoButtonHandler),this.browser.roiTableControl.buttonHandler(!1),super.dispose()}static getColumnFormatConfiguration(t){return!0===t?[{label:"Chr",width:"20%"},{label:"Start",width:"15%"},{label:"End",width:"15%"},{label:"Description",width:"30%"},{label:"ROI Set",width:"20%"}]:[{label:"Chr",width:"25%"},{label:"Start",width:"20%"},{label:"End",width:"20%"},{label:"Description",width:"35%"}]}static gotoButtonHandler(t){t.stopPropagation();const e=this.tableDOM.querySelectorAll(".igv-roi-table-row-selected"),i=[];for(let t of e){const{locus:e}=Jb(t.dataset.region);i.push(e)}for(let t of this.tableDOM.querySelectorAll(".igv-roi-table-row"))t.classList.remove("igv-roi-table-row-selected");this.setTableRowSelectionState(!1),i.length>0&&this.browser.search(i.join(" "))}}class ey{constructor(t,e){this.browser=t,this.container=_e.div({class:"igv-roi-menu-next-gen"}),e.appendChild(this.container);const i=_e.div();this.container.appendChild(i),ki.attachDialogCloseHandlerWithParent(i,(()=>this.container.style.display="none")),this.body=_e.div(),this.container.appendChild(this.body),this.container.style.display="none"}async present(t,e,i,n,r){iy(this.body);const s=await this.browser.roiManager.findUserDefinedRegionWithKey(r.dataset.region),o=_e.div();this.body.appendChild(o);const a="Description",l=s.name||a;o.innerText=l,o.setAttribute("title",l),a===l?o.classList.add("igv-roi-placeholder"):o.classList.remove("igv-roi-placeholder");const h=_e.div();this.body.appendChild(h),h.innerText="Set Description",h.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none";const e={label:"Description",value:s.name||"",callback:()=>{const t=this.browser.inputDialog.value||"";s.name=t.trim(),this.container.style.display="none",this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(e,t)}));const c=_e.div();this.body.appendChild(c),c.innerText="Delete Region",c.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(r.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex"}async __present(t,e,i,n,r){iy(this.container);const s=await this.browser.roiManager.findUserDefinedRegionWithKey(r.dataset.region);let o;o=_e.div({class:"igv-roi-menu-row-edit-description"}),this.container.appendChild(o),o.addEventListener("click",(t=>{t.stopPropagation()}));const a="description-input",l=document.createElement("label");o.appendChild(l),l.setAttribute("for",a),l.innerText="Description:";const h=document.createElement("input");o.appendChild(h),h.setAttribute("type","text"),h.setAttribute("name",a),h.setAttribute("placeholder",""),h.value=s.name||"",h.addEventListener("change",(async t=>{t.stopPropagation(),(await this.browser.roiManager.findUserDefinedRegionWithKey(r.dataset.region)).name=h.value,h.blur(),this.container.style.display="none",await this.browser.roiManager.repaintTable()})),o=_e.div({class:"igv-roi-menu-row"}),o.innerText="Delete region",this.container.appendChild(o),o.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none",this.browser.roiManager.deleteUserDefinedRegionWithKey(r.dataset.region,this.browser.columnContainer)})),this.container.style.left=`${t}px`,this.container.style.top=`${e}px`,this.container.style.display="flex",n.addEventListener("click",(t=>{t.stopPropagation(),this.container.style.display="none"}))}dispose(){this.container.innerHTML=""}}function iy(t){for(;t.firstChild;)t.removeChild(t.firstChild)}class ny{constructor(t,e){this.name=t.name,this.featureSource=t.featureSource||$c(t,e),this.color=t.color||qc}async getFeatures(t,e,i){return this.featureSource.getFeatures({chr:t,start:e,end:i})}draw(t){const{context:e,bpPerPixel:i,bpStart:n,pixelTop:r,pixelHeight:s,pixelWidth:o,features:a}=t;if(!a)return;const l=n+o*i+1;for(let{start:t,end:o}of a){if(ol)break;const{x:a,width:h}=Zc(t,o,n,i);na.fillRect(e,a,r,h,s,{fillStyle:this.color})}}}class ry{constructor(t,e){this.browser=e,this.button=_e.div({class:"igv-navbar-button"}),t.appendChild(this.button),this.button.textContent="ROI Table",this.button.addEventListener("click",(()=>{this.buttonHandler(!e.roiTableVisible)})),this.browser=e,this.setVisibility(e.showROITableButton),this.setState(e.roiTableVisible)}buttonHandler(t){this.browser.roiTableVisible=t,this.setState(this.browser.roiTableVisible),this.browser.setROITableVisibility(this.browser.roiTableVisible)}setVisibility(t){!0===t?this.show():this.hide()}setState(t){!0===t?this.button.classList.add("igv-navbar-button-clicked"):this.button.classList.remove("igv-navbar-button-clicked")}show(){this.button.style.display="block",this.setState(this.browser.roiTableVisible)}hide(){this.button.style.display="none"}}class sy{constructor(t,e){this.config=t,this.guid=_e.guid(),this.namespace=".browser_"+this.guid,this.parent=e,this.root=_e.div({class:"igv-container"}),e.appendChild(this.root),this.alert=new sa(this.root),this.columnContainer=_e.div({class:"igv-column-container"}),this.root.appendChild(this.columnContainer),this.menuPopup=new sf(this.columnContainer),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:"rgb(0,0,150)",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},this.addMouseHandlers(),this.setControls(t)}initialize(t){t.gtex&&(Sd.gtexLoaded=!0),this.flanking=t.flanking,this.crossDomainProxy=t.crossDomainProxy,this.formats=t.formats,this.trackDefaults=t.trackDefaults,this.nucleotideColors=t.nucleotideColors||$a;for(let t of Object.keys(this.nucleotideColors))this.nucleotideColors[t.toLowerCase()]=this.nucleotideColors[t];this.trackLabelsVisible=t.showTrackLabels,this.roiTableVisible=t.showROITable,this.showROITableButton=t.showROITableButton,this.isCenterLineVisible=t.showCenterGuide,this.cursorGuideVisible=t.showCursorGuide,this.showSampleNames=t.showSampleNames,this.showSampleNameButton=t.showSampleNameButton,this.sampleNameViewportWidth=t.sampleNameViewportWidth||200,t.search&&(this.searchConfig={type:"json",url:t.search.url,coords:void 0===t.search.coords?1:t.search.coords,chromosomeField:t.search.chromosomeField||"chromosome",startField:t.search.startField||"start",endField:t.search.endField||"end",geneField:t.search.geneField||"gene",snpField:t.search.snpField||"snp",resultsField:t.search.resultsField})}setControls(t){const e=this.createStandardControls(t);e.insertBefore(fe(this.columnContainer)),this.$navigation=e,!1===t.showControls&&e.hide()}createStandardControls(t){this.navbarManager=new Rb(this);const e=fe("
",{class:"igv-navbar"});this.$navigation=e;const i=fe("
",{class:"igv-navbar-left-container"});e.append(i);const n=fe("
",{class:"igv-logo"});i.append(n);const r=fe('IGV; ');r.css("width","34px"),r.css("height","32px"),n.append(r),this.$current_genome=fe("
",{class:"igv-current-genome"}),i.append(this.$current_genome),this.$current_genome.text("");const s=fe("
",{class:"igv-navbar-genomic-location"});i.append(s),this.chromosomeSelectWidget=new Lb(this,s.get(0)),void 0===t.showChromosomeWidget&&(t.showChromosomeWidget=!0),!0===t.showChromosomeWidget?this.chromosomeSelectWidget.show():this.chromosomeSelectWidget.hide();const o=fe("
",{class:"igv-locus-size-group"});s.append(o);const a=fe("
",{class:"igv-search-container"});o.append(a),this.$searchInput=fe("",{class:"igv-search-input",type:"text",placeholder:"Locus Search"}),a.append(this.$searchInput),this.$searchInput.change((()=>this.doSearch(this.$searchInput.val())));const l=_e.div({class:"igv-search-icon-container"});a.append(fe(l)),l.appendChild(_i.createIcon("search")),l.addEventListener("click",(()=>this.doSearch(this.$searchInput.val()))),this.windowSizePanel=new Bb(o.get(0),this);const h=fe("
",{class:"igv-navbar-right-container"});e.append(h);const c=fe('
');if(h.append(c),this.$toggle_button_container=c,this.cursorGuide=new Nb(this.columnContainer,this),this.cursorGuideButton=new Fb(this,c.get(0)),this.centerLineButton=new Ob(this,c.get(0)),this.setTrackLabelVisibility(t.showTrackLabels),this.trackLabelControl=new Db(c.get(0),this),this.roiTableControl=new ry(c.get(0),this),this.sampleNameControl=new Pb(c.get(0),this),!0===t.showSVGButton&&(this.svgSaveControl=new Hb(c.get(0),this)),t.customButtons)for(let e of t.customButtons)new Zb(c.get(0),this,e);return this.zoomWidget=new Vb(this,h.get(0)),!1===t.showNavigation&&this.$navigation.hide(),this.inputDialog=new Mi(this.root),this.inputDialog.container.id=`igv-input-dialog-${_e.guid()}`,this.dataRangeDialog=new Hi(this,fe(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${_e.guid()}`,this.genericColorPicker=new Pi({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${_e.guid()}`,e}getSampleNameViewportWidth(){return!1===this.showSampleNames?0:this.sampleNameViewportWidth}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}addTrackToFactory(t,e){xb(t,e)}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let t of this.referenceFrameList)if("all"===t.chr.toLowerCase())return!0;return!1}currentLoci(){const t=t=>`${t.chr}:${t.start+1}-${t.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?"":1===this.referenceFrameList.length?t(this.referenceFrameList[0]):this.referenceFrameList.map((e=>t(e)))}toSVG(){const{y:t,width:e,height:i}=this.columnContainer.getBoundingClientRect(),n=new ll({width:e,height:8e3,backdropColor:"white",multiLocusGap:0,viewbox:{x:0,y:0,width:e,height:8e3}}),r={deltaX:0,deltaY:-t};for(let t of this.trackViews)t.renderSVGContext(n,r);return this.roiManager.renderSVGContext(n,r),n.setHeight(i),n.getSerializedSvg(!0)}renderSVG(t){const e=this.toSVG();return t.empty(),t.append(e),e}saveSVGtoFile(t){let e=this.toSVG();t.$container&&(t.$container.empty(),t.$container.append(e)),Qi(t.filename||"igvjs.svg",URL.createObjectURL(new Blob([e],{type:"application/octet-stream"})))}async loadSession(t){let e;return this.roiSets=[],e=t.url||t.file?await async function(t){const e=t.url||t.file;if(t.url&&(t.url.startsWith("blob:")||t.url.startsWith("data:"))){const e=sy.uncompressSession(t.url);return JSON.parse(e)}{let i=t.filename;if(i||(i=t.url?await ua(t.url):t.file.name),i.endsWith(".xml")){const t=ul.KNOWN_GENOMES,i=await zo.loadString(e);return new kb(i,t)}return i.endsWith(".json")?zo.loadJson(e):void 0}}(t):t,this.loadSessionObject(e)}async loadSessionObject(t){this.cleanHouseForSession(),this.showSampleNames=t.showSampleNames||!1,this.sampleNameControl.setState(!0===this.showSampleNames),t.sampleNameViewportWidth&&(this.sampleNameViewportWidth=t.sampleNameViewportWidth),pa(this.columnContainer,"igv-axis-column"),pa(this.columnContainer,"igv-sample-name-column"),pa(this.columnContainer,"igv-scrollbar-column"),pa(this.columnContainer,"igv-track-drag-column"),pa(this.columnContainer,"igv-gear-menu-column");const e=t.reference||t.genome;if(!e)return void console.warn("No genome or reference object specified");const i=await ul.expandReference(this.alert,e);await this.loadReference(i,t.locus),this.centerLineList=this.createCenterLineList(this.columnContainer);let n=0;if(!1!==t.showIdeogram){const t=new zf(this);t.id="ideogram";const e=new hf(this,this.columnContainer,t),{$viewport:i}=e.viewports[0];n=function(t){t="string"==typeof t?document.querySelector(t):t;const e=window.getComputedStyle(t),i=parseFloat(e.marginTop)+parseFloat(e.marginBottom),n=t.offsetHeight;return Math.ceil(i+n)}(i.get(0)),this.trackViews.push(e)}if(!1!==t.showRuler&&this.trackViews.push(new hf(this,this.columnContainer,new qb(this))),t.gtexSelections)for(let e of this.referenceFrameList)for(let i of Object.keys(t.gtexSelections)){const n=t.gtexSelections[i].gene,r=t.gtexSelections[i].snp;e.selection=new Tb(n,r)}this.roiManager&&this.roiManager.dispose();const r=new ey(this,this.columnContainer),s={browser:this,parent:this.columnContainer,headerTitle:"Regions of Interest",dismissHandler:()=>this.roiTableControl.buttonHandler(!1),gotoButtonHandler:ty.gotoButtonHandler};if(t.roi){const e=t.roi.map((t=>new Gc(t,this.genome))),i=e.filter((({name:t})=>void 0!==t&&t.length>0));s.columnFormat=ty.getColumnFormatConfiguration(i.length>0);const o=new ty(s);this.roiManager=new Yb(this,r,o,n,e)}else{s.columnFormat=ty.getColumnFormatConfiguration(!1);const t=new ty(s);this.roiManager=new Yb(this,r,t,n,void 0)}await this.roiManager.initialize();const o=i.tracks||[],a=t.tracks?o.concat(t.tracks):o;0===a.filter((t=>"sequence"===t.type&&!t.url&&!t.fastaURL)).length&&a.push({type:"sequence",order:qa});let l=1;for(let t of a)void 0===t.order&&(t.order=l++);await this.loadTrackList(a);for(let t of this.trackViews.filter((t=>"ruler"===t.track.type||"ideogram"===t.track.type)))t.updateViews();this.updateUIWithReferenceFrameList()}createCenterLineList(t){const e=t.querySelectorAll(".igv-center-line");for(let t=0;tt.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}updateNavbarDOMWithGenome(t){let e=t.id&&t.id.length<10?t.id:"";this.$current_genome.text(e),this.$current_genome.attr("title",t.id||""),this.chromosomeSelectWidget.update(t)}async loadGenome(t){const e=await ul.expandReference(this.alert,t);await this.loadReference(e,void 0);const i=e.tracks||[];return 0===i.filter((t=>"sequence"===t.type)).length&&i.push({type:"sequence",order:qa}),await this.loadTrackList(i),await this.updateViews(),this.genome}updateUIWithReferenceFrameList(){const t=this.referenceFrameList;this.updateLocusSearchWidget();const e=this.isMultiLocusWholeGenomeView()||ul.isWholeGenomeView(t[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),e),hy(this.trackViews,this.trackLabelsVisible),this.setCenterLineAndCenterLineButtonVisibility(!ul.isWholeGenomeView(t[0].chr))}setTrackLabelVisibility(t){hy(this.trackViews,t)}setROITableVisibility(t){!0===t?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(t){t?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(t){this.cursorGuide.customMouseHandler=t}setCenterLineVisibility(t){for(let e of this.centerLineList)!0===t?(e.show(),e.repaint()):e.hide()}setCenterLineAndCenterLineButtonVisibility(t){for(let e of this.centerLineList)t&&e.isVisible?e.show():e.container.style.display="none";t&&this.centerLineButton.isVisible?this.centerLineButton.show():this.centerLineButton.button.style.display="none"}async loadTrackList(t){const e=[];for(let i of t)e.push(this._loadTrack(i));const i=await Promise.all(e);return this.trackViews.filter((function(t){return t.track.autoscaleGroup})).length>0&&this.updateViews(),i}async loadTrack(t){const e=this._loadTrack(t);return t.autoscaleGroup&&(await e,this.updateViews()),e}async _loadTrack(t){ji(t)&&(t=JSON.parse(t));try{const e=await this.createTrack(t);if(void 0===e)return;void 0===e.order&&(e.order=this.trackViews.length);const i=new hf(this,this.columnContainer,e);if(this.trackViews.push(i),hy(this.trackViews,this.trackLabelsVisible),this.reorderTracks(),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),"function"==typeof e.postInit)try{i.startSpinner(),await e.postInit()}finally{i.stopSpinner()}return e.autoscaleGroup||(t.sync?await i.updateViews():i.updateViews()),"function"==typeof e.hasSamples&&e.hasSamples()&&!1!==this.config.showSampleNameButton&&this.sampleNameControl.show(),e}catch(e){const i={401:"Access unauthorized",403:"Access forbidden",404:"Not found"};console.error(e);let n=e.message||e.error||e.toString();i.hasOwnProperty(n)&&(n=i[n]),n+=": "+t.url,this.alert.present(new Error(n),void 0)}}async loadROI(t){await this.roiManager.loadROI(t,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const t=await this.roiManager.getUserDefinedROISet();if(void 0===t)return[];const e=await t.getAllFeatures(),i=[];for(let t of Object.values(e))i.push(...t);return i}return[]}getRulerTrackView(){const t=this.trackViews.filter((({track:t})=>"ruler"===t.id));return t.length>0?t[0]:void 0}async createTrack(t){let e=await async function(t){return"function"==typeof t?t():t}(t.url||t.fastaURL);if(ji(e)&&(e=e.trim()),e)if(t.format)t.format=t.format.toLowerCase();else if(t.fastaURL)t.format="fasta";else{let i=t.filename;i||(i=await ua(e));const n=ka(i);"tsv"===n?t.format=await Aa(t):n?t.format=n:"htsget"===t.sourceType&&await cc.inferFormat(t)}let i=t.type?t.type.toLowerCase():void 0;if(!i){if(i=Ca(t),"bedtype"===i){const e=$c(t,this.genome);t._featureSource=e;i=await e.trackType()||"annotation"}t.type=i}if(this.trackDefaults&&i){const e=this.trackDefaults[i];if(e)for(let i in e)e.hasOwnProperty(i)&&void 0===t[i]&&(t[i]=e[i])}const n=function(t,e,i){let n;switch(t){case"annotation":case"genes":case"fusionjuncspan":case"snp":n="feature";break;case"seg":case"maf":case"mut":n="seg";break;case"junctions":case"splicejunctions":n="junction";break;default:n=t}return _b.has(n)?_b.get(n)(e,i):void 0}(i,t,this);if(void 0!==n)return t.roi&&t.roi.length>0&&(n.roiSets=t.roi.map((t=>new ny(t,this.genome)))),n;this.alert.present(new Error(`Error creating track. Could not determine track type for file: ${t.url||t}`),void 0)}reorderTracks(){this.trackViews.sort((function(t,e){const i=t=>"ideogram"===t.track.id?1:"ruler"===t.track.id?2:3,n=i(t),r=i(e);return n===r?(t.track.order||0)-(e.track.order||0):n-r}));for(let{axis:t,viewports:e,sampleNameViewport:i,outerScroll:n,dragHandle:r,gearContainer:s}of this.trackViews){t.remove();for(let{$viewport:t}of e)t.detach();i.viewport.remove(),n.remove(),r.remove(),s.remove()}const t=this.columnContainer.querySelectorAll(".igv-column");for(let{axis:e,viewports:i,sampleNameViewport:n,outerScroll:r,dragHandle:s,gearContainer:o}of this.trackViews){this.columnContainer.querySelector(".igv-axis-column").appendChild(e);for(let e=0;et.track&&t.track.name)).map((t=>t.track.name))}removeTrackByName(t){const e=this.trackViews.slice();for(let i of e)t===i.track.name&&this.removeTrack(i.track)}removeTrack(t){for(let e of this.trackViews)if(t===e.track){this._removeTrack(e.track);break}}_removeTrack(t){t.disposed||(this.trackViews.splice(this.trackViews.indexOf(t.trackView),1),this.fireEvent("trackremoved",[t]),this.fireEvent("trackorderchanged",[this.getTrackOrder()]),t.trackView&&t.trackView.dispose())}removeAllTracks(){const t=[];for(let e of this.trackViews)"ruler"!==e.track.id&&"ideogram"!==e.track.id?(this.fireEvent("trackremoved",[e.track]),e.dispose()):t.push(e);this.trackViews=t}findTracks(t,e){let i="function"==typeof t?e=>t(e.track):i=>e===i.track[t];return this.trackViews.filter(i).map((t=>t.track))}setTrackHeight(t){this.trackHeight=t,this.trackViews.forEach((function(e){e.setTrackHeight(t)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((t=>t.bpPerPixel<0))){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel=(e.end-e.start)/t}if(this.referenceFrameList){const t=this.isMultiLocusWholeGenomeView()||ul.isWholeGenomeView(this.referenceFrameList[0].chr);this.navbarManager.navbarDidResize(this.$navigation.width(),t)}oy.call(this),await this.updateViews()}async updateViews(){const t=this.trackViews;this.updateLocusSearchWidget();for(let t of this.centerLineList)t.repaint();if(this.dragObject)for(let e of t)await e.updateViews();else{const r={},s=[];for(let i of t){const t=i.track.autoscaleGroup;if(t){var e=r[t];e||(e=[],r[t]=e),e.push(i)}else s.push(i)}if(Object.entries(r).length>0){const t=Object.keys(r);for(let e of t){const t=r[e],s=[];for(let e of t)s.push(e.getInViewFeatures());const o=await Promise.all(s);var i,n=[];for(let t of o)n=n.concat(t);i=ha(n);const a=[];for(let e of t)e.track.dataRange=i,e.track.autoscale=!1,a.push(e.updateViews());await Promise.all(a)}}await Promise.all(s.map((t=>t.updateViews())))}}repaintViews(){for(let t of this.trackViews)t.repaintViews()}updateLocusSearchWidget(){if(!this.referenceFrameList)return;const t=this.referenceFrameList,e=this.calculateViewportWidth(this.referenceFrameList.length);for(let i of t)i.end=i.start+i.bpPerPixel*e;this.chromosomeSelectWidget.select.value=1===t.length?this.referenceFrameList[0].chr:"";const i=this.referenceFrameList.map((t=>t.getLocusString())).join(" ");this.$searchInput.val(i),this.fireEvent("locuschange",[this.referenceFrameList])}calculateViewportWidth(t){let{width:e}=this.columnContainer.getBoundingClientRect();return e-=50+this.getSampleNameViewportWidth()+14+12+28,e-=5*(t-1),Math.floor(e/t)}getCenterLineXOffset(){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleNameViewportWidth()+14+12+28,Math.floor(t/2+50)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(t,e,i){if(!this.referenceFrameList)return;const n=this.calculateViewportWidth(this.referenceFrameList.length);let r=i?[i]:this.referenceFrameList;for(let i of r)i.zoomWithScaleFactor(this,t,n,e)}async addMultiLocusPanel(t,e,i,n){if(!this.referenceFrameList)return;const r=this.calculateViewportWidth(1+this.referenceFrameList.length),s=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=s;const o=(i-e)/r,a=new Eb(this.genome,t,e,i,o),l=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,h=1+l,{$viewport:c}=this.trackViews[0].viewports[l],u=(t=>{const e=_e.div({class:"igv-column-shim"});ma(e,t);const i=_e.div({class:"igv-column"});return ma(i,e),i})(c.get(0).parentElement);if(h===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let t of this.trackViews){const e=tf(t,u,a);t.viewports.push(e)}}else{this.referenceFrameList.splice(h,0,a);for(let t of this.trackViews){const e=tf(t,u,a);t.viewports.splice(h,0,e)}}this.centerLineList=this.createCenterLineList(this.columnContainer),oy.call(this),await this.updateViews(!0)}async removeMultiLocusPanel(t){const e=this.referenceFrameList.indexOf(t),{$viewport:i}=this.trackViews[0].viewports[e];((t,e)=>{const i=0===t?e.nextElementSibling:e.previousElementSibling;e.remove(),i.remove()})(e,i.parent().get(0));for(let{viewports:t}of this.trackViews)t[e].dispose(),t.splice(e,1);if(this.referenceFrameList.splice(e,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let t of this.getRulerTrackView().viewports)t.dismissLocusLabel();const n=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(n)}async gotoMultilocusPanel(t){const e=this.referenceFrameList.indexOf(t);this.columnContainer.querySelectorAll(".igv-column").forEach(((t,i)=>{i===e||t.remove()})),this.columnContainer.querySelectorAll(".igv-column-shim").forEach((t=>t.remove()));for(let t of this.trackViews){const i=t.viewports[e];t.viewports.filter(((t,i)=>i!==e)).forEach((t=>t.dispose())),t.viewports=[i]}const i=this.calculateViewportWidth(1);t.bpPerPixel=(t.end-t.start)/i,this.referenceFrameList=[t],this.trackViews.forEach((({viewports:t})=>t.forEach((t=>t.setWidth(i))))),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(t){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=t;for(let{viewports:t}of this.trackViews)for(let i of t)i.setWidth(e);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(t,e,i){await this.search(t+":"+e+"-"+i)}async doSearch(t,e){const i=await this.search(t,e);return i||this.alert.present(new Error(`Unrecognized locus: ${t} `)),i}async search(t,e){const i=await async function(t,e){if(void 0===e||""===e.trim())return;(e&&"all"===e.trim().toLowerCase()||"*"===e)&&(e="all");const i=e.split(" ");let n=t.searchConfig||Mb,r=[];const s=async i=>{let r=function(t,e){const i=e.split("\t");if(i.length>=3)try{const e=t.genome.getChromosomeName(i[0]),n=parseInt(i[1].replace(/,/g,""),10)-1,r=parseInt(i[2].replace(/,/g,""),10);if(!isNaN(n)&&!isNaN(r))return{chr:e,start:n,end:r}}catch(t){}const n=e.split(":"),r=n[0];if("all"===r&&t.genome.getChromosome(r))return{chr:r,start:0,end:t.genome.getChromosome(r).bpLength};if(void 0!==t.genome.getChromosome(r)){const e={chr:t.genome.getChromosomeName(r),start:0,end:t.genome.getChromosome(r).bpLength};if(n.length>1){let i,r=n[1].split("-");if(r.length>2){if(!n[1].startsWith("-"))return;{const t=n[1].indexOf("-",1);t>0&&(r=[n[1].substring(0,t),n[1].substring(t+1)])}}if(i=r[0].replace(/,/g,""),isNaN(i))return;if(e.start=parseInt(i,10)-1,e.end=e.start+1,1===r.length&&(e.start-=20,e.end+=20),2===r.length){if(i=r[1].replace(/,/g,""),isNaN(i))return;if(e.end=parseInt(i,10),e.start<0&&!t.isSoftclipped()){const t=-e.start;e.start+=t,e.end+=t}}}return e}}(t,i);if(!r){const n=t.genome.featureDB.get(i.toUpperCase());n&&(r={chr:n.chr,start:n.start,end:n.end,gene:n.name,locusSearchString:e})}if(!r&&t.config&&!1!==t.config.search)try{r=await async function(t,e,i){let n=i.url.replace("$FEATURE$",e.toUpperCase());n.indexOf("$GENOME$")>-1&&(n=n.replace("$GENOME$",t.genome.id?t.genome.id:"hg19"));const r=i.timeout?{timeout:i.timeout}:void 0,s=function(t,e,i){let n;if(n="plain"===i.type?function(t,e){const i=[],n=[];return qi(e).forEach((function(t){""===t||i.push(t)})),i.forEach((function(e){var i,r,s,o,a=e.split("\t");a.length>=3&&(s=(r=a[1].split(":"))[1].split("-"),i=a[2].trim(),o={gene:a[0],chromosome:t.genome.getChromosomeName(r[0].trim()),start:parseInt(s[0].replace(/,/g,"")),end:parseInt(s[1].replace(/,/g,"")),type:"gtex"===i?"snp":"gene"},n.push(o))})),n}(t,e):JSON.parse(e),i.resultsField&&(n=n[i.resultsField]),n&&0!==n.length){const e=i.chromosomeField||"chromosome",r=i.startField||"start",s=i.endField||"end",o=i.coords||1;let a;a=Array.isArray(n)?n[0]:n,a.hasOwnProperty(e)&&a.hasOwnProperty(r)||console.error("Search service results must include chromosome and start fields: "+a);const l=a[e],h=t.genome.getChromosome(l);if(!h)return;const c=h.name;let u=a[r]-o,d=a[s];void 0===d&&(d=u+1);const f={chr:c,start:u,end:d},p=a.type?a.type:"gene";return i.geneField&&"gene"===p&&(f.gene=a[i.geneField]),i.snpField&&"snp"===p&&(f.snp=a[i.snpField]),f}}(t,await zo.loadString(n,r),i);return s&&(s.locusSearchString=e),s}(t,i,n)}catch(t){throw console.error(t),Error("Search service currently unavailable.")}return r};for(let t of i){const e=await s(t);e&&(e.locusSearchString=t,r.push(e))}if(0===r.length){const t=await s(e);t&&(t.locusSearchString=e,r.push(t))}return 0===r.length?void 0:r}(this,t);if(i&&i.length>0){this.referenceFrameList=function(t,e,i,n,r,s){return t.map((t=>{if(i&&t.gene&&(t.start=Math.max(0,t.start-i),t.end+=i),!s){const i=e.getChromosome(t.chr);ca(i.bpLength,t,n)}const o=new Eb(e,t.chr,t.start,t.end,(t.end-t.start)/r);return o.locusSearchString=t.locusSearchString,(t.gene||t.snp)&&(o.selection=new Tb(t.gene,t.snp)),o}))}(i,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(i.length),this.isSoftclipped());for(let t of this.trackViews)t.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(".igv-column-shim, .igv-column").forEach((t=>t.remove())),((t,e)=>{for(let i=0;i1&&i>0&&ga(_e.div({class:"igv-column-shim"}),n)}})(this.columnContainer.querySelector(".igv-sample-name-column"),this.referenceFrameList.length),this.centerLineList=this.createCenterLineList(this.columnContainer);for(let t of this.trackViews)t.addDOMToColumnContainer(this,this.columnContainer,this.referenceFrameList);return this.updateUIWithReferenceFrameList(),e||await this.updateViews(),!0}return!1}async loadSampleInformation(t){var e=t;Yi(t)&&(e=t.name),"fam"===e.substr(e.lastIndexOf(".")+1)&&(this.sampleInformation=await function(t,e){return(new Ab).loadPlinkFile(t,void 0)}(t))}on(t,e){this.eventHandlers[t]||(this.eventHandlers[t]=[]),this.eventHandlers[t].push(e)}un(t,e){this.off(t,e)}off(t,e){if(t)if(e){const i=this.eventHandlers[t];if(i&&0!==i.length){const n=i.indexOf(e);-1!==n&&this.eventHandlers[t].splice(n,1)}else console.warn("No handlers to remove for event: "+t)}else this.eventHandlers[t]=[];else this.eventHandlers={}}fireEvent(t,e,i){const n=this.eventHandlers[t];if(void 0===n||0===n.length)return;const r=i||window;return n.map((function(t){return t.apply(r,e)}))[0]}dispose(){this.removeMouseHandlers();for(let t of this.trackViews)t.dispose()}toJSON(){const t={version:"2.15.11"};if(void 0!==this.showSampleNames&&(t.showSampleNames=this.showSampleNames),200!==this.sampleNameViewportWidth&&(t.sampleNameViewportWidth=this.sampleNameViewportWidth),t.reference=this.genome.toJSON(),t.reference.fastaURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${t.reference.fastaURL.name}.`);if(t.reference.indexURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${t.reference.indexURL.name}.`);const e=[],i={};let n=!1,r=this.trackViews[0];for(let{referenceFrame:t}of r.viewports){const r=t.getLocusString();if(e.push(r),t.selection){const e={gene:t.selection.gene,snp:t.selection.snp};i[r]=e,n=!0}}t.locus=1===e.length?e[0]:e,n&&(t.gtexSelections=i),t.roi=this.roiManager.toJSON();const s=[],o=[];for(let{track:t}of this.trackViews)try{let e;e="function"==typeof t.getState?t.getState():t.config,e&&(e.browser&&delete e.browser,e.order=t.order,s.push(e))}catch(e){console.error(`Track: ${t.name}: ${e}`),o.push(`Track: ${t.name}: ${e}`)}if(o.length>0){let t=1,e="Errors encountered saving session:
";for(let i of o)e+=` (${t++}) ${i.toString()}
`;throw Error(e)}return t.tracks=s,t}compressedSession(){return function(t){const e=new Uint8Array(t.length);for(var i=0;i0?t.substring(0,e):t)+"?sessionURL=blob:"+this.compressedSession()}mouseDownOnViewport(t,e){var i;i=_e.pageCoordinates(t),this.vpMouseDown={viewport:e,lastMouseX:i.x,mouseDownX:i.x,lastMouseY:i.y,mouseDownY:i.y,referenceFrame:e.referenceFrame}}cancelTrackPan(){const t=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,t&&t.viewport.referenceFrame.start!==t.start&&(this.updateViews(),this.fireEvent("trackdragend"))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((t=>!0===t.track.showSoftClips))}startTrackDrag(t){this.dragTrack=t}updateTrackDrag(t){if(t&&this.dragTrack){const e=this.dragTrack,i=this.trackViews.indexOf(t),n=this.trackViews.indexOf(e),r=this.trackViews;r[i]=e,r[n]=t;const s=this.trackViews[i].track.order;this.trackViews[n].track.order=s;const o=r.length;let a=s;if(i0;t--){const e=r[t].track;if(!(e.order>=a))break;e.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=e.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent("trackorderchanged",[this.getTrackOrder()])):this.dragTrack=void 0}addMouseHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers()}removeMouseHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers()}addWindowResizeHandler(){this.boundWindowResizeHandler=oy.bind(this),window.addEventListener("resize",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener("resize",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=ly.bind(this),this.root.addEventListener("mouseup",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener("mouseup",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=ly.bind(this),this.root.addEventListener("mouseleave",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener("mouseleave",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=ay.bind(this),this.boundColumnContainerTouchMoveHandler=ay.bind(this),this.boundColumnContainerMouseLeaveHandler=ly.bind(this),this.boundColumnContainerMouseUpHandler=ly.bind(this),this.boundColumnContainerTouchEndHandler=ly.bind(this),this.columnContainer.addEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener("touchend",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener("mousemove",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener("touchmove",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener("mouseleave",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener("mouseup",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener("touchend",this.boundColumnContainerTouchEndHandler)}static uncompressSession(t){let e;if(t.indexOf("/gzip;base64")>0){e=bo(t);let i="";for(let t of e)i+=String.fromCharCode(t);return i}return function(t){t=t.replace(/\./g,"+").replace(/_/g,"/").replace(/-/g,"=");const e=atob(t),i=[];for(let t=0;t{const r=t.data,s=r.mate;function o(t){t.chr=i.genome.getChromosomeName(t.refName);let e=!1;for(let n of i.referenceFrameList){const i=qu.fromLocusString(n.getLocusString());if(i.contains(t)){e=!0;break}if(i.overlaps(t)){n.extend(t),e=!0;break}}if(!e){const e=2e3,n=(t.start+t.end)/2;i.addMultiLocusPanel(t.chr,n-e,n+e)}}o(r),o(s)}})),this.circularViewControl=new Gb(this.$toggle_button_container.get(0),this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:wd(this.genome)}),this.circularViewVisible=e,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(t){this.circularView&&(this.circularView.visible=t,this.circularViewControl.setState(t))}}async function oy(){if(!this.referenceFrameList)return;const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let e of this.referenceFrameList){const i=this.referenceFrameList.indexOf(e),{chr:n,genome:r}=e,{bpLength:s}=r.getChromosome(e.chr),o=e.toBP(t);ul.isWholeGenomeView(n)||o>s?e.bpPerPixel=s/t:e.end=e.start+e.toBP(t);for(let{viewports:e}of this.trackViews)e[i].setWidth(t)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function ay(t){t.preventDefault();const{x:e,y:i}=_e.pageCoordinates(t);if(this.vpMouseDown){const{viewport:t,referenceFrame:n}=this.vpMouseDown,r=Math.abs(e-this.vpMouseDown.mouseDownX)>Math.abs(i-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(r)this.vpMouseDown.mouseDownX&&Math.abs(e-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:t,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(i-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const e=t.$viewport.height(),i=t.trackView.maxViewportContentHeight();this.vpMouseDown.r=e/i}if(this.dragObject){const i=!this.isSoftclipped();let r=this.vpMouseDown.lastMouseX-e;n.shiftPixels(r,t.$viewport.width(),i)&&this.updateViews(),this.fireEvent("trackdrag")}if(this.isScrolling){const e=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-i);t.trackView.moveScroller(e)}this.vpMouseDown.lastMouseX=e,this.vpMouseDown.lastMouseY=i}}function ly(t){this.cancelTrackPan(),this.endTrackDrag()}function hy(t,e){for(let{viewports:i}of t)for(let t of i)t.$trackLabel&&(0===i.indexOf(t)&&!0===e?t.$trackLabel.show():t.$trackLabel.hide())}let cy=[];const uy=zo.setApiKey;!function(){var t=document.createElement("style");t.setAttribute("type","text/css"),t.innerHTML='.igv-navbar {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n box-sizing: border-box;\n width: 100%;\n color: #444;\n font-size: 12px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n line-height: 32px;\n padding-left: 8px;\n padding-right: 8px;\n margin-top: 2px;\n margin-bottom: 6px;\n height: 32px;\n border-style: solid;\n border-radius: 3px;\n border-width: thin;\n border-color: #bfbfbf;\n background-color: #f3f3f3;\n}\n.igv-navbar .igv-navbar-left-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 32px;\n line-height: 32px;\n}\n.igv-navbar .igv-navbar-left-container .igv-logo {\n width: 34px;\n height: 32px;\n margin-right: 8px;\n}\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\n height: 32px;\n margin-left: 4px;\n margin-right: 4px;\n user-select: none;\n line-height: 32px;\n vertical-align: middle;\n text-align: center;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 100%;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n height: 100%;\n width: 125px;\n margin-right: 4px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\n display: block;\n cursor: pointer;\n width: 100px;\n height: 75%;\n outline: none;\n font-size: 12px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n margin-left: 8px;\n height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n width: 210px;\n height: 22px;\n line-height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\n cursor: text;\n width: 85%;\n height: 22px;\n line-height: 22px;\n font-size: 12px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n text-align: left;\n padding-left: 8px;\n margin-right: 8px;\n outline: none;\n border-style: solid;\n border-radius: 3px;\n border-width: thin;\n border-color: #bfbfbf;\n background-color: white;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\n cursor: pointer;\n height: 16px;\n width: 16px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\n margin-left: 4px;\n user-select: none;\n}\n.igv-navbar .igv-navbar-right-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 32px;\n line-height: 32px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n height: 100%;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div {\n margin-left: 0;\n margin-right: 4px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div:last-child {\n margin-left: 0;\n margin-right: 0;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-750 {\n display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\n color: #737373;\n font-size: 18px;\n height: 32px;\n line-height: 32px;\n margin-left: 8px;\n user-select: none;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\n cursor: pointer;\n margin-left: unset;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\n height: 24px;\n width: 24px;\n margin-left: unset;\n margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\n height: 24px;\n width: 24px;\n margin-left: 8px;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\n display: block;\n height: fit-content;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\n display: block;\n width: 125px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\n display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\n color: #737373;\n font-size: 18px;\n height: 32px;\n line-height: 32px;\n margin-left: 8px;\n user-select: none;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\n cursor: pointer;\n margin-left: unset;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\n height: 24px;\n width: 24px;\n margin-left: unset;\n margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\n height: 24px;\n width: 24px;\n margin-left: 8px;\n margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\n width: 0;\n height: 0;\n display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\n width: 0;\n height: 0;\n display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\n display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\n display: none;\n}\n\n.igv-navbar-button {\n display: block;\n box-sizing: unset;\n padding-left: 6px;\n padding-right: 6px;\n height: 18px;\n text-transform: capitalize;\n user-select: none;\n line-height: 18px;\n text-align: center;\n vertical-align: middle;\n font-family: "Open Sans", sans-serif;\n font-size: 11px;\n font-weight: 200;\n color: #737373;\n background-color: #f3f3f3;\n border-color: #737373;\n border-style: solid;\n border-width: thin;\n border-radius: 6px;\n}\n\n.igv-navbar-button-clicked {\n color: white;\n background-color: #737373;\n}\n\n.igv-navbar-button:hover {\n cursor: pointer;\n}\n\n.igv-zoom-in-notice-container {\n z-index: 1024;\n position: absolute;\n top: 8px;\n left: 50%;\n transform: translate(-50%, 0%);\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n background-color: white;\n}\n.igv-zoom-in-notice-container > div {\n padding-left: 4px;\n padding-right: 4px;\n padding-top: 2px;\n padding-bottom: 2px;\n width: 100%;\n height: 100%;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n color: #3f3f3f;\n}\n\n.igv-zoom-in-notice {\n position: absolute;\n top: 10px;\n left: 50%;\n}\n.igv-zoom-in-notice div {\n position: relative;\n left: -50%;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n color: #3f3f3f;\n background-color: rgba(255, 255, 255, 0.51);\n z-index: 64;\n}\n\n.igv-container-spinner {\n position: absolute;\n top: 90%;\n left: 50%;\n transform: translate(-50%, -50%);\n z-index: 1024;\n width: 24px;\n height: 24px;\n pointer-events: none;\n color: #737373;\n}\n\n.igv-multi-locus-close-button {\n position: absolute;\n top: 2px;\n right: 0;\n padding-left: 2px;\n padding-right: 2px;\n width: 12px;\n height: 12px;\n color: #666666;\n background-color: white;\n z-index: 1000;\n}\n.igv-multi-locus-close-button > svg {\n vertical-align: top;\n}\n\n.igv-multi-locus-close-button:hover {\n cursor: pointer;\n color: #434343;\n}\n\n.igv-multi-locus-ruler-label {\n z-index: 64;\n position: absolute;\n top: 2px;\n left: 0;\n width: 100%;\n height: 12px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n}\n.igv-multi-locus-ruler-label > div {\n font-family: "Open Sans", sans-serif;\n font-size: 12px;\n color: rgb(16, 16, 16);\n background-color: white;\n}\n.igv-multi-locus-ruler-label > div {\n cursor: pointer;\n}\n\n.igv-multi-locus-ruler-label-square-dot {\n z-index: 64;\n position: absolute;\n left: 50%;\n top: 5%;\n transform: translate(-50%, 0%);\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\n width: 14px;\n height: 14px;\n}\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\n margin-left: 16px;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n color: rgb(16, 16, 16);\n}\n\n.igv-ruler-sweeper {\n display: none;\n pointer-events: none;\n position: absolute;\n top: 26px;\n bottom: 0;\n left: 0;\n width: 0;\n z-index: 99999;\n background-color: rgba(68, 134, 247, 0.25);\n}\n\n.igv-ruler-tooltip {\n pointer-events: none;\n z-index: 128;\n position: absolute;\n top: 0;\n left: 0;\n width: 1px;\n height: 32px;\n background-color: transparent;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-ruler-tooltip > div {\n pointer-events: none;\n width: 128px;\n height: auto;\n padding: 1px;\n color: #373737;\n font-size: 10px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n background-color: white;\n border-style: solid;\n border-width: thin;\n border-color: #373737;\n}\n\n.igv-track-label {\n position: absolute;\n left: 8px;\n top: 8px;\n width: auto;\n height: auto;\n max-width: 50%;\n padding-left: 4px;\n padding-right: 4px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n text-align: center;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n border-color: #444;\n border-radius: 2px;\n border-style: solid;\n border-width: thin;\n background-color: white;\n z-index: 128;\n cursor: pointer;\n}\n\n.igv-track-label:hover,\n.igv-track-label:focus,\n.igv-track-label:active {\n background-color: #e8e8e8;\n}\n\n.igv-track-label-popup-shim {\n padding-left: 8px;\n padding-right: 8px;\n padding-top: 4px;\n}\n\n.igv-center-line {\n display: none;\n pointer-events: none;\n position: absolute;\n top: 0;\n bottom: 0;\n left: 50%;\n transform: translateX(-50%);\n z-index: 8;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n border-left-style: dashed;\n border-left-width: thin;\n border-right-style: dashed;\n border-right-width: thin;\n}\n\n.igv-center-line-wide {\n background-color: rgba(0, 0, 0, 0);\n border-left-color: rgba(127, 127, 127, 0.51);\n border-right-color: rgba(127, 127, 127, 0.51);\n}\n\n.igv-center-line-thin {\n background-color: rgba(0, 0, 0, 0);\n border-left-color: rgba(127, 127, 127, 0.51);\n border-right-color: rgba(0, 0, 0, 0);\n}\n\n.igv-cursor-guide-horizontal {\n display: none;\n pointer-events: none;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n position: absolute;\n left: 0;\n right: 0;\n top: 50%;\n height: 1px;\n z-index: 1;\n margin-left: 50px;\n margin-right: 54px;\n border-top-style: dotted;\n border-top-width: thin;\n border-top-color: rgba(127, 127, 127, 0.76);\n}\n\n.igv-cursor-guide-vertical {\n pointer-events: none;\n user-select: none;\n -moz-user-select: none;\n -webkit-user-select: none;\n position: absolute;\n top: 0;\n bottom: 0;\n left: 50%;\n width: 1px;\n z-index: 1;\n border-left-style: dotted;\n border-left-width: thin;\n border-left-color: rgba(127, 127, 127, 0.76);\n display: none;\n}\n\n.igv-user-feedback {\n position: fixed;\n top: 50%;\n left: 50%;\n transform: translate(-50%, -50%);\n width: 512px;\n height: 360px;\n z-index: 2048;\n background-color: white;\n border-color: #a2a2a2;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n color: #444;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-user-feedback div:first-child {\n position: relative;\n height: 24px;\n width: 100%;\n background-color: white;\n border-bottom-color: #a2a2a2;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n position: absolute;\n top: 2px;\n width: 16px;\n height: 16px;\n background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n cursor: pointer;\n right: 8px;\n}\n.igv-user-feedback div:last-child {\n width: 100%;\n height: calc(100% - 24px);\n border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n width: auto;\n height: auto;\n margin: 8px;\n}\n\n.igv-generic-dialog-container {\n position: absolute;\n top: 0;\n left: 0;\n width: 300px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n z-index: 2048;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\n color: #373737;\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin-top: 8px;\n padding-left: 8px;\n overflow-wrap: break-word;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\n margin-top: 8px;\n width: 95%;\n height: 24px;\n color: #373737;\n line-height: 24px;\n padding-left: 8px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\n width: 30%;\n height: 100%;\n font-size: 16px;\n text-align: right;\n padding-right: 8px;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n width: 50%;\n font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input {\n margin-top: 8px;\n width: calc(100% - 16px);\n height: 24px;\n color: #373737;\n line-height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: "Open Sans", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\n width: 100%;\n height: 28px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\n margin-top: 32px;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\n margin-left: 32px;\n margin-right: 0;\n background-color: #5ea4e0;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\n margin-left: 0;\n margin-right: 32px;\n background-color: #c4c4c4;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f;\n}\n\n.igv-generic-container {\n position: absolute;\n top: 0;\n left: 0;\n z-index: 2048;\n background-color: white;\n cursor: pointer;\n display: flex;\n flex-direction: row;\n flex-wrap: wrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-generic-container div:first-child {\n cursor: move;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n height: 24px;\n width: 100%;\n background-color: #dddddd;\n}\n.igv-generic-container div:first-child i {\n display: block;\n color: #5f5f5f;\n cursor: pointer;\n width: 14px;\n height: 14px;\n margin-right: 8px;\n margin-bottom: 4px;\n}\n\n.igv-menu-popup {\n position: absolute;\n top: 0;\n left: 0;\n width: max-content;\n z-index: 4096;\n cursor: pointer;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n color: #4b4b4b;\n background: white;\n border-radius: 4px;\n border-color: #7F7F7F;\n border-style: solid;\n border-width: thin;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-end;\n text-align: left;\n}\n.igv-menu-popup > div:not(:first-child) {\n width: 100%;\n}\n.igv-menu-popup > div:not(:first-child) > div {\n background: white;\n}\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\n padding-left: 4px;\n padding-right: 4px;\n}\n.igv-menu-popup > div:not(:first-child) > div:last-child {\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-color: transparent;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-menu-popup > div:not(:first-child) > div:hover {\n background: #efefef;\n}\n\n.igv-menu-popup-shim {\n padding-left: 8px;\n padding-right: 8px;\n padding-bottom: 1px;\n padding-top: 1px;\n}\n\n.igv-menu-popup-header {\n position: relative;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-color: transparent;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-menu-popup-header div {\n margin-right: 4px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-menu-popup-header div:hover {\n cursor: pointer;\n color: #444;\n}\n\n.igv-menu-popup-check-container {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n width: 100%;\n height: 20px;\n margin-right: 4px;\n background-color: transparent;\n}\n.igv-menu-popup-check-container div {\n padding-top: 2px;\n padding-left: 8px;\n}\n.igv-menu-popup-check-container div:first-child {\n position: relative;\n width: 12px;\n height: 12px;\n}\n.igv-menu-popup-check-container div:first-child svg {\n position: absolute;\n width: 12px;\n height: 12px;\n}\n\n.igv-user-feedback {\n position: fixed;\n top: 50%;\n left: 50%;\n transform: translate(-50%, -50%);\n width: 512px;\n height: 360px;\n z-index: 2048;\n background-color: white;\n border-color: #a2a2a2;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: medium;\n font-weight: 400;\n color: #444;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n}\n.igv-user-feedback div:first-child {\n position: relative;\n height: 24px;\n width: 100%;\n background-color: white;\n border-bottom-color: #a2a2a2;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n position: absolute;\n top: 2px;\n width: 16px;\n height: 16px;\n background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n cursor: pointer;\n right: 8px;\n}\n.igv-user-feedback div:last-child {\n width: 100%;\n height: calc(100% - 24px);\n border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n width: auto;\n height: auto;\n margin: 8px;\n}\n\n.igv-loading-spinner-container {\n z-index: 1024;\n position: absolute;\n top: 50%;\n left: 50%;\n transform: translate(-50%, -50%);\n width: 32px;\n height: 32px;\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center;\n}\n.igv-loading-spinner-container > div {\n box-sizing: border-box;\n width: 100%;\n height: 100%;\n border-radius: 50%;\n border: 4px solid rgba(128, 128, 128, 0.5);\n border-top-color: rgb(255, 255, 255);\n animation: spin 1s ease-in-out infinite;\n -webkit-animation: spin 1s ease-in-out infinite;\n}\n\n@keyframes spin {\n to {\n -webkit-transform: rotate(360deg);\n transform: rotate(360deg);\n }\n}\n@-webkit-keyframes spin {\n to {\n -webkit-transform: rotate(360deg);\n transform: rotate(360deg);\n }\n}\n.igv-roi-menu-next-gen {\n position: absolute;\n z-index: 512;\n font-family: "Open Sans", sans-serif;\n font-size: small;\n font-weight: 400;\n color: #4b4b4b;\n background-color: white;\n width: 192px;\n border-radius: 4px;\n border-color: #7F7F7F;\n border-style: solid;\n border-width: thin;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-menu-next-gen > div:first-child {\n height: 24px;\n border-top-color: transparent;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n}\n.igv-roi-menu-next-gen > div:first-child > div {\n margin-right: 4px;\n height: 12px;\n width: 12px;\n color: #7F7F7F;\n}\n.igv-roi-menu-next-gen > div:first-child > div:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-roi-menu-next-gen > div:last-child {\n background-color: white;\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-color: transparent;\n border-bottom-style: solid;\n border-bottom-width: 0;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n text-align: start;\n vertical-align: middle;\n}\n.igv-roi-menu-next-gen > div:last-child > div {\n height: 24px;\n padding-left: 4px;\n border-bottom-style: solid;\n border-bottom-width: thin;\n border-bottom-color: #7f7f7f;\n}\n.igv-roi-menu-next-gen > div:last-child > div:not(:first-child):hover {\n background-color: rgba(127, 127, 127, 0.1);\n}\n.igv-roi-menu-next-gen > div:last-child div:first-child {\n font-style: italic;\n text-align: center;\n padding-right: 4px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n}\n.igv-roi-menu-next-gen > div:last-child > div:last-child {\n border-bottom-width: 0;\n border-bottom-color: transparent;\n}\n\n.igv-roi-placeholder {\n font-style: normal;\n color: rgba(75, 75, 75, 0.6);\n}\n\n.igv-roi-table {\n position: absolute;\n z-index: 1024;\n width: min-content;\n max-width: 1600px;\n border-color: #7f7f7f;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n font-size: 12px;\n font-weight: 400;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n cursor: default;\n}\n.igv-roi-table > div {\n height: 24px;\n font-size: 14px;\n text-align: start;\n vertical-align: middle;\n line-height: 24px;\n}\n.igv-roi-table > div:first-child {\n border-color: transparent;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-top-width: 0;\n border-bottom-color: #7f7f7f;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee;\n cursor: move;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n}\n.igv-roi-table > div:first-child > div:first-child {\n text-align: center;\n white-space: nowrap;\n text-overflow: ellipsis;\n overflow: hidden;\n margin-left: 4px;\n margin-right: 4px;\n width: calc(100% - 4px - 12px);\n}\n.igv-roi-table > div:first-child > div:last-child {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7f7f7f;\n}\n.igv-roi-table > div:first-child > div:last-child > svg {\n display: block;\n}\n.igv-roi-table > div:first-child > div:last-child:hover {\n cursor: pointer;\n color: #444;\n}\n.igv-roi-table > .igv-roi-table-description {\n padding: 4px;\n margin-left: 4px;\n word-break: break-all;\n overflow-y: auto;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n background-color: transparent;\n}\n.igv-roi-table > .igv-roi-table-goto-explainer {\n margin-top: 5px;\n margin-left: 4px;\n color: #7F7F7F;\n font-style: italic;\n height: 24px;\n border-top: solid lightgray;\n background-color: transparent;\n}\n.igv-roi-table > .igv-roi-table-column-titles {\n height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: stretch;\n align-items: stretch;\n padding-right: 16px;\n background-color: white;\n border-top-color: #7f7f7f;\n border-top-style: solid;\n border-top-width: thin;\n border-bottom-color: #7f7f7f;\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div {\n font-size: 14px;\n vertical-align: middle;\n line-height: 24px;\n text-align: left;\n margin-left: 4px;\n height: 24px;\n overflow: hidden;\n text-overflow: ellipsis;\n border-right-color: #7f7f7f;\n border-right-style: solid;\n border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\n border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container {\n overflow: auto;\n resize: both;\n max-width: 1600px;\n height: 360px;\n background-color: transparent;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\n height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: stretch;\n align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\n font-size: 14px;\n vertical-align: middle;\n line-height: 24px;\n text-align: left;\n margin-left: 4px;\n height: 24px;\n white-space: nowrap;\n overflow: hidden;\n text-overflow: ellipsis;\n border-right-color: transparent;\n border-right-style: solid;\n border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\n border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table > div:last-child {\n height: 32px;\n line-height: 32px;\n border-top-color: #7f7f7f;\n border-top-style: solid;\n border-top-width: thin;\n border-bottom-color: transparent;\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-width: 0;\n background-color: #eee;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center;\n}\n\n.igv-roi-table-row-selected {\n background-color: rgba(0, 0, 0, 0.125);\n}\n\n.igv-roi-table-button {\n cursor: pointer;\n height: 20px;\n user-select: none;\n line-height: 20px;\n text-align: center;\n vertical-align: middle;\n font-family: "Open Sans", sans-serif;\n font-size: 13px;\n font-weight: 400;\n color: black;\n padding-left: 6px;\n padding-right: 6px;\n background-color: rgb(239, 239, 239);\n border-color: black;\n border-style: solid;\n border-width: thin;\n border-radius: 3px;\n}\n\n.igv-roi-table-button:hover {\n font-weight: 400;\n background-color: rgba(0, 0, 0, 0.13);\n}\n\n.igv-roi-region {\n z-index: 64;\n position: absolute;\n top: 0;\n bottom: 0;\n pointer-events: none;\n overflow: visible;\n margin-top: 44px;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-region > div {\n position: relative;\n width: 100%;\n height: 8px;\n pointer-events: auto;\n}\n\n.igv-roi-menu {\n position: absolute;\n z-index: 1024;\n width: 144px;\n border-color: #7f7f7f;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: "Open Sans", sans-serif;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n}\n.igv-roi-menu > div:not(:last-child) {\n border-bottom-color: rgba(128, 128, 128, 0.5);\n border-bottom-style: solid;\n border-bottom-width: thin;\n}\n.igv-roi-menu > div:first-child {\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-top-color: transparent;\n border-top-style: solid;\n border-top-width: 0;\n}\n.igv-roi-menu > div:last-child {\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n border-bottom-color: transparent;\n border-bottom-style: solid;\n border-bottom-width: 0;\n}\n\n.igv-roi-menu-row {\n height: 24px;\n padding-left: 8px;\n font-size: small;\n text-align: start;\n vertical-align: middle;\n line-height: 24px;\n background-color: white;\n}\n\n.igv-roi-menu-row-edit-description {\n width: -webkit-fill-available;\n font-size: small;\n text-align: start;\n vertical-align: middle;\n background-color: white;\n padding-left: 4px;\n padding-right: 4px;\n padding-bottom: 4px;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: stretch;\n align-items: stretch;\n}\n.igv-roi-menu-row-edit-description > label {\n margin-left: 2px;\n margin-bottom: 0;\n display: block;\n width: -webkit-fill-available;\n}\n.igv-roi-menu-row-edit-description > input {\n display: block;\n margin-left: 2px;\n margin-right: 2px;\n margin-bottom: 1px;\n width: -webkit-fill-available;\n}\n\n.igv-container {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n padding-top: 4px;\n user-select: none;\n -webkit-user-select: none;\n -ms-user-select: none;\n}\n\n.igv-viewport {\n position: relative;\n margin-top: 5px;\n line-height: 1;\n overflow-x: hidden;\n overflow-y: hidden;\n}\n\n.igv-viewport-content {\n position: relative;\n width: 100%;\n}\n.igv-viewport-content > canvas {\n position: relative;\n display: block;\n}\n\n.igv-column-container {\n position: relative;\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: stretch;\n width: 100%;\n}\n\n.igv-column-shim {\n width: 1px;\n margin-left: 2px;\n margin-right: 2px;\n background-color: #545453;\n}\n\n.igv-column {\n position: relative;\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n}\n\n.igv-axis-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 50px;\n}\n.igv-axis-column > div {\n margin-top: 5px;\n width: 100%;\n}\n\n.igv-sample-name-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n}\n\n.igv-scrollbar-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 14px;\n}\n.igv-scrollbar-column > div {\n position: relative;\n margin-top: 5px;\n width: 14px;\n}\n.igv-scrollbar-column > div > div {\n cursor: pointer;\n position: absolute;\n top: 0;\n left: 2px;\n width: 8px;\n border-width: 1px;\n border-style: solid;\n border-color: #c4c4c4;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-left-radius: 4px;\n border-bottom-right-radius: 4px;\n}\n.igv-scrollbar-column > div > div:hover {\n background-color: #c4c4c4;\n}\n\n.igv-track-drag-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 12px;\n background-color: white;\n}\n.igv-track-drag-column > .igv-track-drag-handle {\n z-index: 512;\n position: relative;\n cursor: pointer;\n margin-top: 5px;\n width: 100%;\n border-style: solid;\n border-width: 0;\n border-top-right-radius: 6px;\n border-bottom-right-radius: 6px;\n background-color: #c4c4c4;\n}\n.igv-track-drag-column .igv-track-drag-handle-hover {\n background-color: #787878;\n}\n.igv-track-drag-column > .igv-track-drag-shim {\n position: relative;\n margin-top: 5px;\n width: 100%;\n border-style: solid;\n border-width: 0;\n}\n\n.igv-gear-menu-column {\n position: relative;\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: flex-start;\n box-sizing: border-box;\n height: 100%;\n width: 28px;\n}\n.igv-gear-menu-column > div {\n display: flex;\n flex-direction: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n margin-top: 5px;\n width: 100%;\n background: white;\n}\n.igv-gear-menu-column > div > div {\n position: relative;\n margin-top: 4px;\n width: 16px;\n height: 16px;\n color: #7F7F7F;\n}\n.igv-gear-menu-column > div > div:hover {\n cursor: pointer;\n color: #444;\n}\n\n/*# sourceMappingURL=dom.css.map */\n',document.head.append(t)}();const dy=zo.oauth;var fy={TrackUtils:Ia,IGVGraphics:na,MenuUtils:Ui,DataRangeDialog:Hi,createTrack:async function(t,e){return await sy.prototype.createTrack.call(e,t)},createBrowser:async function(t,e){void 0===e&&(e={}),ul.KNOWN_GENOMES||await ul.initializeGenomes(e),function(t){void 0===t.minimumBases&&(t.minimumBases=40),void 0===t.showIdeogram&&(t.showIdeogram=!0),void 0===t.showCircularView&&(t.showCircularView=!1),void 0===t.showCircularViewButton&&(t.showCircularViewButton=!1),void 0===t.showTrackLabelButton&&(t.showTrackLabelButton=!0),void 0===t.showTrackLabels&&(t.showTrackLabels=!0),void 0===t.showROITableButton&&(t.showROITableButton=!1),void 0===t.showROITable&&(t.showROITable=!1),void 0===t.showCursorTrackingGuideButton&&(t.showCursorTrackingGuideButton=!0),void 0===t.showCursorGuide&&(t.showCursorGuide=t.showCursorTrackingGuide||!1),void 0===t.showCenterGuideButton&&(t.showCenterGuideButton=!0),void 0===t.showCenterGuide&&(t.showCenterGuide=!1),void 0===t.showSampleNames&&(t.showSampleNames=!1),void 0===t.showSVGButton&&(t.showSVGButton=!0),void 0===t.showControls&&(t.showControls=!0),void 0===t.showNavigation&&(t.showNavigation=!0),void 0===t.showRuler&&(t.showRuler=!0),void 0===t.flanking&&(t.flanking=1e3),void 0===t.pairsSupported&&(t.pairsSupported=!0),t.tracks||(t.tracks=[])}(e),e.queryParametersSupported&&function(t){var e,i,n,r,s,o,a,l;let h,c,u;if({},e=(o=window.location.href).indexOf("?"),i=o.lastIndexOf("#"),e>=0)for(i<0&&(i=o.length),n=e+1;ne&&(i.indexURL=c[e]),u&&u.length>e&&(i.name=u[e]),t.tracks.push(i)}}}(e),e.apiKey&&zo.setApiKey(e.apiKey),e.oauthToken&&zo.setOauthToken(e.oauthToken),e.clientId&&!Ro()&&await async function(t){if(!google.accounts.oauth2.initTokenClient)throw new Error("Google accounts token client not loaded (https://accounts.google.com/gsi/client)");if(Ro())throw new Error("Google client is already initialized");const e={client_id:t.client_id,scope:t.scope||"https://www.googleapis.com/auth/userinfo.profile",state:t.state||"igv",error:t=>{throw new Error(t.type)},hint:t.hint,hosted_domain:t.hosted_domain},i=google.accounts.oauth2.initTokenClient(e);google.igv={tokenClient:i,apiKey:t.apiKey}}({clientId:e.clientId,apiKey:e.apiKey,scope:"https://www.googleapis.com/auth/userinfo.profile"});const i=new sy(e,t);return cy.push(i),e.sessionURL?await i.loadSession({url:e.sessionURL}):await i.loadSessionObject(e),i.navbarManager.navbarDidResize(i.$navigation.width()),i},removeBrowser:function(t){t.dispose(),t.root.remove(),cy=cy.filter((e=>e!==t))},removeAllBrowsers:function(){for(let t of cy)t.dispose(),t.root.remove();cy=[]},visibilityChange:async function(){for(let t of cy)await t.visibilityChange()},setGoogleOauthToken:function(t){return zo.setOauthToken(t)},setOauthToken:function(t,e){return zo.setOauthToken(t,e)},oauth:dy,version:function(){return"2.15.11"},setApiKey:uy,registerFileFormats:Ta};return fy}));var uo,fo,po=function(e){function i(t){var e;return function(t,e){if(!(t instanceof e))throw new TypeError("Cannot call a class as a function")}(this,i),(e=ao(this,i,[t])).browser=null,e}var n,r;return function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Super expression must either be null or a function");t.prototype=Object.create(e&&e.prototype,{constructor:{value:t,writable:!0,configurable:!0}}),Object.defineProperty(t,"prototype",{writable:!1}),e&&co(t,e)}(i,e),n=i,(r=[{key:"componentDidMount",value:function(){this.initializeIGV(this.props.genomeReference||"hg19")}},{key:"componentDidUpdate",value:function(t){this.props.genomeReference!==t.genomeReference&&this.initializeIGV(this.props.genomeReference),this.props.crisprResults!==t.crisprResults&&this.updateTracks(this.props.crisprResults)}},{key:"initializeIGV",value:function(e){var i=this,n=document.getElementById("igvDiv"),r={genome:e};t.createBrowser(n,r).then((function(t){i.browser=t,i.updateTracks(i.props.crisprResults)}))}},{key:"updateTracks",value:function(t){if(this.browser&&t&&t.length>0){this.browser.removeAllTracks();var e="track name='CRISPR Targets' description='CRISPR Cas9 Predictions'\n";e+=t.map((function(t){var e=t[0],i=t[1],n=t[2],r=1===t[3]?"+":"-",s="gRNA: ".concat(t[4]," Score: ").concat(t[5]);return"".concat(e,"\t").concat(i,"\t").concat(n,"\t").concat(s,"\t0\t").concat(r)})).join("\n");var i=new Blob([e],{type:"text/plain"}),n={name:"CRISPR Targets",url:URL.createObjectURL(i),format:"bed",type:"annotation",indexed:!1};this.browser.loadTrack(n)}}},{key:"render",value:function(){return u.createElement("div",{id:"igvDiv",style:{height:"500px"}})}}])&&so(n.prototype,r),Object.defineProperty(n,"prototype",{writable:!1}),i}(u.Component);uo=po,fo=function(t){function e(e){var i=t.call(this,e)||this;return i.componentDidMount=function(){eo.events.addEventListener(eo.RENDER_EVENT,i.onRenderEvent),eo.setComponentReady()},i.componentDidUpdate=function(){null!=i.state.componentError&&eo.setFrameHeight()},i.componentWillUnmount=function(){eo.events.removeEventListener(eo.RENDER_EVENT,i.onRenderEvent)},i.onRenderEvent=function(t){i.setState({renderData:t.detail})},i.state={renderData:void 0,componentError:void 0},i}return no(e,t),e.prototype.render=function(){return null!=this.state.componentError?u.createElement("div",null,u.createElement("h1",null,"Component Error"),u.createElement("span",null,this.state.componentError.message)):null==this.state.renderData?null:u.createElement(uo,{width:window.innerWidth,disabled:this.state.renderData.disabled,args:this.state.renderData.args,theme:this.state.renderData.theme})},e.getDerivedStateFromError=function(t){return{componentError:t}},e}(u.PureComponent),f()(fo,uo)})()})(); \ No newline at end of file