jbrowse2: x/static/js/4864.28cfc358.chunk.js.map annotate

annotate x/static/js/4864.28cfc358.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

author	fubar
date	Sat, 05 Oct 2024 23:58:05 +0000
parents
children

rev	line source
125 49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566 fubar parents: diff changeset	1 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BED from '@gmod/bed'\nimport {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Region, Feature, isGzip } from '@jbrowse/core/util'\nimport IntervalTree from '@flatten-js/interval-tree'\nimport { unzip } from '@gmod/bgzf-filehandle'\n\n// locals\nimport { featureData } from '../util'\n\nexport default class BedAdapter extends BaseFeatureDataAdapter {\n protected bedFeatures?: Promise<{\n header: string\n features: Record<string, string[]>\n parser: BED\n columnNames: string[]\n scoreColumn: string\n colRef: number\n colStart: number\n colEnd: number\n }>\n\n protected intervalTrees: Record<\n string,\n Promise<IntervalTree \| undefined> \| undefined\n > = {}\n\n public static capabilities = ['getFeatures', 'getRefNames']\n\n private async loadDataP(opts: BaseOptions = {}) {\n const pm = this.pluginManager\n const bedLoc = this.getConf('bedLocation')\n const buf = await openLocation(bedLoc, pm).readFile(opts)\n const buffer = isGzip(buf) ? await unzip(buf) : buf\n // 512MB max chrome string length is 512MB\n if (buffer.length > 536_870_888) {\n throw new Error('Data exceeds maximum string length (512MB)')\n }\n const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)\n const lines = data.split(/\\n\|\\r\\n\|\\r/).filter(f => !!f)\n const headerLines = []\n let i = 0\n for (; i < lines.length && lines[i]!.startsWith('#'); i++) {\n headerLines.push(lines[i])\n }\n const header = headerLines.join('\\n')\n const features = {} as Record<string, string[]>\n for (; i < lines.length; i++) {\n const line = lines[i]!\n const tab = line.indexOf('\\t')\n const refName = line.slice(0, tab)\n if (!features[refName]) {\n features[refName] = []\n }\n features[refName].push(line)\n }\n\n const autoSql = this.getConf('autoSql') as string\n const parser = new BED({ autoSql })\n const columnNames = this.getConf('columnNames')\n const scoreColumn = this.getConf('scoreColumn')\n const colRef = this.getConf('colRef')\n const colStart = this.getConf('colStart')\n const colEnd = this.getConf('colEnd')\n\n return {\n header,\n features,\n parser,\n columnNames,\n scoreColumn,\n colRef,\n colStart,\n colEnd,\n }\n }\n\n private async loadData(opts: BaseOptions = {}) {\n if (!this.bedFeatures) {\n this.bedFeatures = this.loadDataP(opts).catch((e: unknown) => {\n this.bedFeatures = undefined\n throw e\n })\n }\n\n return this.bedFeatures\n }\n\n public async getRefNames(opts: BaseOptions = {}) {\n const { features } = await this.loadData(opts)\n return Object.keys(features)\n }\n\n async getHeader(opts: BaseOptions = {}) {\n const { header } = await this.loadData(opts)\n return header\n }\n\n async getNames() {\n const { header, columnNames } = await this.loadData()\n if (columnNames.length) {\n return columnNames\n }\n const defs = header.split(/\\n\|\\r\\n\|\\r/).filter(f => !!f)\n const defline = defs.at(-1)\n return defline?.includes('\\t')\n ? defline\n .slice(1)\n .split('\\t')\n .map(field => field.trim())\n : undefined\n }\n\n private async loadFeatureIntervalTreeHelper(refName: string) {\n const { colRef, colStart, colEnd, features, parser, scoreColumn } =\n await this.loadData()\n const lines = features[refName]\n if (!lines) {\n return undefined\n }\n const names = await this.getNames()\n\n const intervalTree = new IntervalTree()\n const ret = lines.map((f, i) => {\n const uniqueId = `${this.id}-${refName}-${i}`\n return featureData(\n f,\n colRef,\n colStart,\n colEnd,\n scoreColumn,\n parser,\n uniqueId,\n names,\n )\n })\n\n for (const obj of ret) {\n intervalTree.insert([obj.get('start'), obj.get('end')], obj)\n }\n return intervalTree\n }\n\n private async loadFeatureIntervalTree(refName: string) {\n if (!this.intervalTrees[refName]) {\n this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(\n refName,\n ).catch((e: unknown) => {\n this.intervalTrees[refName] = undefined\n throw e\n })\n }\n return this.intervalTrees[refName]\n }\n\n public getFeatures(query: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { start, end, refName } = query\n const intervalTree = await this.loadFeatureIntervalTree(refName)\n intervalTree?.search([start, end]).forEach(f => {\n observer.next(f)\n })\n observer.complete()\n }, opts.signal)\n }\n\n public freeResources(): void {}\n}\n","import BED from '@gmod/bed'\nimport { SimpleFeature } from '@jbrowse/core/util'\n\nexport interface MinimalFeature {\n type: string\n start: number\n end: number\n refName: string\n [key: string]: unknown\n}\nexport interface TranscriptFeat extends MinimalFeature {\n thickStart: number\n thickEnd: number\n blockCount: number\n blockSizes: number[]\n chromStarts: number[]\n refName: string\n strand?: number\n subfeatures: MinimalFeature[]\n}\n\nexport function ucscProcessedTranscript(feature: TranscriptFeat) {\n const {\n subfeatures: oldSubfeatures,\n thickStart,\n thickEnd,\n blockCount,\n blockSizes,\n chromStarts,\n refName,\n strand = 0,\n ...rest\n } = feature\n\n if (!thickStart \|\| !thickEnd \|\| !strand) {\n return feature\n }\n\n const subfeatures: MinimalFeature[] = []\n oldSubfeatures\n .filter(child => child.type === 'block')\n .sort((a, b) => a.start - b.start)\n .forEach(block => {\n const start = block.start\n const end = block.end\n if (thickStart >= end) {\n // left-side UTR\n const prime = strand > 0 ? 'five' : 'three'\n subfeatures.push({\n type: `${prime}_prime_UTR`,\n start,\n end,\n refName,\n })\n } else if (thickStart > start && thickStart < end && thickEnd >= end) {\n // UTR \| CDS\n const prime = strand > 0 ? 'five' : 'three'\n subfeatures.push(\n {\n type: `${prime}_prime_UTR`,\n start,\n end: thickStart,\n refName,\n },\n {\n type: 'CDS',\n start: thickStart,\n end,\n refName,\n },\n )\n } else if (thickStart <= start && thickEnd >= end) {\n // CDS\n subfeatures.push({\n type: 'CDS',\n start,\n end,\n refName,\n })\n } else if (thickStart > start && thickStart < end && thickEnd < end) {\n // UTR \| CDS \| UTR\n const leftPrime = strand > 0 ? 'five' : 'three'\n const rightPrime = strand > 0 ? 'three' : 'five'\n subfeatures.push(\n {\n type: `${leftPrime}_prime_UTR`,\n start,\n end: thickStart,\n refName,\n },\n {\n type: 'CDS',\n start: thickStart,\n end: thickEnd,\n refName,\n },\n {\n type: `${rightPrime}_prime_UTR`,\n start: thickEnd,\n end,\n refName,\n },\n )\n } else if (thickStart <= start && thickEnd > start && thickEnd < end) {\n // CDS \| UTR\n const prime = strand > 0 ? 'three' : 'five'\n subfeatures.push(\n {\n type: 'CDS',\n start,\n end: thickEnd,\n refName,\n },\n {\n type: `${prime}_prime_UTR`,\n start: thickEnd,\n end,\n refName,\n },\n )\n } else if (thickEnd <= start) {\n // right-side UTR\n const prime = strand > 0 ? 'three' : 'five'\n subfeatures.push({\n type: `${prime}_prime_UTR`,\n start,\n end,\n refName,\n })\n }\n })\n\n return { ...rest, strand, type: 'mRNA', refName, subfeatures }\n}\n\nfunction defaultParser(fields: string[], line: string) {\n const obj = Object.fromEntries(\n line.split('\\t').map((f, i) => [fields[i]!, f] as const),\n )\n const {\n blockStarts,\n blockCount,\n chromStarts,\n thickEnd,\n thickStart,\n blockSizes,\n ...rest\n } = obj\n\n return {\n ...rest,\n blockStarts: blockStarts?.split(',').map(r => +r),\n chromStarts: chromStarts?.split(',').map(r => +r),\n blockSizes: blockSizes?.split(',').map(r => +r),\n thickStart: thickStart ? +thickStart : undefined,\n thickEnd: thickEnd ? +thickEnd : undefined,\n blockCount: blockCount ? +blockCount : undefined,\n } as Record<string, unknown>\n}\n\nexport function makeBlocks({\n start,\n uniqueId,\n refName,\n chromStarts,\n blockCount,\n blockSizes,\n blockStarts,\n}: {\n blockCount: number\n start: number\n uniqueId: string\n refName: string\n chromStarts?: number[]\n blockSizes: number[]\n blockStarts?: number[]\n}) {\n const subfeatures = []\n const starts = chromStarts \|\| blockStarts \|\| []\n for (let b = 0; b < blockCount; b++) {\n const bmin = (starts[b] \|\| 0) + start\n const bmax = bmin + (blockSizes[b] \|\| 0)\n subfeatures.push({\n uniqueId: `${uniqueId}-${b}`,\n start: bmin,\n end: bmax,\n refName,\n type: 'block',\n })\n }\n return subfeatures\n}\nexport function featureData(\n line: string,\n colRef: number,\n colStart: number,\n colEnd: number,\n scoreColumn: string,\n parser: BED,\n uniqueId: string,\n names?: string[],\n) {\n const l = line.split('\\t')\n const refName = l[colRef]!\n const start = +l[colStart]!\n const colSame = colStart === colEnd ? 1 : 0\n const end = +l[colEnd]! + colSame\n const data = names\n ? defaultParser(names, line)\n : parser.parseLine(line, { uniqueId })\n\n const {\n blockCount,\n blockSizes,\n blockStarts,\n chromStarts,\n thickStart,\n thickEnd,\n type,\n score,\n chrom: _1,\n chromStart: _2,\n chromEnd: _3,\n ...rest\n } = data\n const subfeatures = blockCount\n ? makeBlocks({\n start,\n uniqueId,\n refName,\n chromStarts,\n blockCount,\n blockSizes,\n blockStarts,\n })\n : []\n const f = {\n ...rest,\n type,\n score: scoreColumn ? +data[scoreColumn] : score,\n start,\n end,\n refName,\n uniqueId,\n subfeatures,\n }\n return new SimpleFeature({\n id: uniqueId,\n data: isUcscProcessedTranscript(data)\n ? ucscProcessedTranscript({\n thickStart: thickStart!,\n thickEnd: thickEnd!,\n blockCount: blockCount!,\n blockSizes: blockSizes!,\n chromStarts: chromStarts,\n ...f,\n })\n : f,\n })\n}\n\nexport function isUcscProcessedTranscript(f: {\n thickStart?: number\n blockCount?: number\n strand?: number\n}) {\n return f.thickStart && f.blockCount && f.strand !== 0\n}\n"],"names":["BedAdapter","BaseFeatureDataAdapter","intervalTrees","loadDataP","opts","pm","this","pluginManager","bedLoc","getConf","buf","openLocation","readFile","buffer","isGzip","unzip","length","Error","lines","TextDecoder","fatal","decode","split","filter","f","headerLines","i","startsWith","push","header","join","features","line","tab","indexOf","refName","slice","autoSql","parser","BED","columnNames","scoreColumn","colRef","colStart","colEnd","loadData","bedFeatures","catch","e","undefined","getRefNames","Object","keys","getHeader","getNames","defline","at","includes","map","field","trim","loadFeatureIntervalTreeHelper","names","intervalTree","IntervalTree","ret","uniqueId","id","featureData","obj","insert","get","loadFeatureIntervalTree","getFeatures","query","ObservableCreate","async","start","end","search","forEach","observer","next","complete","signal","freeResources","ucscProcessedTranscript","feature","subfeatures","oldSubfeatures","thickStart","thickEnd","blockCount","blockSizes","chromStarts","strand","rest","child","type","sort","a","b","block","prime","leftPrime","rightPrime","makeBlocks","blockStarts","starts","bmin","bmax","l","colSame","data","fields","fromEntries","r","defaultParser","parseLine","score","chrom","_1","chromStart","_2","chromEnd","_3","SimpleFeature","isUcscProcessedTranscript"],"sourceRoot":""}

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49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

fubar

parents:

diff changeset

1 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BED from '@gmod/bed'\nimport {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Region, Feature, isGzip } from '@jbrowse/core/util'\nimport IntervalTree from '@flatten-js/interval-tree'\nimport { unzip } from '@gmod/bgzf-filehandle'\n\n// locals\nimport { featureData } from '../util'\n\nexport default class BedAdapter extends BaseFeatureDataAdapter {\n protected bedFeatures?: Promise<{\n header: string\n features: Record<string, string[]>\n parser: BED\n columnNames: string[]\n scoreColumn: string\n colRef: number\n colStart: number\n colEnd: number\n }>\n\n protected intervalTrees: Record<\n string,\n Promise<IntervalTree | undefined> | undefined\n > = {}\n\n public static capabilities = ['getFeatures', 'getRefNames']\n\n private async loadDataP(opts: BaseOptions = {}) {\n const pm = this.pluginManager\n const bedLoc = this.getConf('bedLocation')\n const buf = await openLocation(bedLoc, pm).readFile(opts)\n const buffer = isGzip(buf) ? await unzip(buf) : buf\n // 512MB max chrome string length is 512MB\n if (buffer.length > 536_870_888) {\n throw new Error('Data exceeds maximum string length (512MB)')\n }\n const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)\n const lines = data.split(/\\n|\\r\\n|\\r/).filter(f => !!f)\n const headerLines = []\n let i = 0\n for (; i < lines.length && lines[i]!.startsWith('#'); i++) {\n headerLines.push(lines[i])\n }\n const header = headerLines.join('\\n')\n const features = {} as Record<string, string[]>\n for (; i < lines.length; i++) {\n const line = lines[i]!\n const tab = line.indexOf('\\t')\n const refName = line.slice(0, tab)\n if (!features[refName]) {\n features[refName] = []\n }\n features[refName].push(line)\n }\n\n const autoSql = this.getConf('autoSql') as string\n const parser = new BED({ autoSql })\n const columnNames = this.getConf('columnNames')\n const scoreColumn = this.getConf('scoreColumn')\n const colRef = this.getConf('colRef')\n const colStart = this.getConf('colStart')\n const colEnd = this.getConf('colEnd')\n\n return {\n header,\n features,\n parser,\n columnNames,\n scoreColumn,\n colRef,\n colStart,\n colEnd,\n }\n }\n\n private async loadData(opts: BaseOptions = {}) {\n if (!this.bedFeatures) {\n this.bedFeatures = this.loadDataP(opts).catch((e: unknown) => {\n this.bedFeatures = undefined\n throw e\n })\n }\n\n return this.bedFeatures\n }\n\n public async getRefNames(opts: BaseOptions = {}) {\n const { features } = await this.loadData(opts)\n return Object.keys(features)\n }\n\n async getHeader(opts: BaseOptions = {}) {\n const { header } = await this.loadData(opts)\n return header\n }\n\n async getNames() {\n const { header, columnNames } = await this.loadData()\n if (columnNames.length) {\n return columnNames\n }\n const defs = header.split(/\\n|\\r\\n|\\r/).filter(f => !!f)\n const defline = defs.at(-1)\n return defline?.includes('\\t')\n ? defline\n .slice(1)\n .split('\\t')\n .map(field => field.trim())\n : undefined\n }\n\n private async loadFeatureIntervalTreeHelper(refName: string) {\n const { colRef, colStart, colEnd, features, parser, scoreColumn } =\n await this.loadData()\n const lines = features[refName]\n if (!lines) {\n return undefined\n }\n const names = await this.getNames()\n\n const intervalTree = new IntervalTree()\n const ret = lines.map((f, i) => {\n const uniqueId = `${this.id}-${refName}-${i}`\n return featureData(\n f,\n colRef,\n colStart,\n colEnd,\n scoreColumn,\n parser,\n uniqueId,\n names,\n )\n })\n\n for (const obj of ret) {\n intervalTree.insert([obj.get('start'), obj.get('end')], obj)\n }\n return intervalTree\n }\n\n private async loadFeatureIntervalTree(refName: string) {\n if (!this.intervalTrees[refName]) {\n this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(\n refName,\n ).catch((e: unknown) => {\n this.intervalTrees[refName] = undefined\n throw e\n })\n }\n return this.intervalTrees[refName]\n }\n\n public getFeatures(query: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { start, end, refName } = query\n const intervalTree = await this.loadFeatureIntervalTree(refName)\n intervalTree?.search([start, end]).forEach(f => {\n observer.next(f)\n })\n observer.complete()\n }, opts.signal)\n }\n\n public freeResources(): void {}\n}\n","import BED from '@gmod/bed'\nimport { SimpleFeature } from '@jbrowse/core/util'\n\nexport interface MinimalFeature {\n type: string\n start: number\n end: number\n refName: string\n [key: string]: unknown\n}\nexport interface TranscriptFeat extends MinimalFeature {\n thickStart: number\n thickEnd: number\n blockCount: number\n blockSizes: number[]\n chromStarts: number[]\n refName: string\n strand?: number\n subfeatures: MinimalFeature[]\n}\n\nexport function ucscProcessedTranscript(feature: TranscriptFeat) {\n const {\n subfeatures: oldSubfeatures,\n thickStart,\n thickEnd,\n blockCount,\n blockSizes,\n chromStarts,\n refName,\n strand = 0,\n ...rest\n } = feature\n\n if (!thickStart || !thickEnd || !strand) {\n return feature\n }\n\n const subfeatures: MinimalFeature[] = []\n oldSubfeatures\n .filter(child => child.type === 'block')\n .sort((a, b) => a.start - b.start)\n .forEach(block => {\n const start = block.start\n const end = block.end\n if (thickStart >= end) {\n // left-side UTR\n const prime = strand > 0 ? 'five' : 'three'\n subfeatures.push({\n type: `${prime}_prime_UTR`,\n start,\n end,\n refName,\n })\n } else if (thickStart > start && thickStart < end && thickEnd >= end) {\n // UTR | CDS\n const prime = strand > 0 ? 'five' : 'three'\n subfeatures.push(\n {\n type: `${prime}_prime_UTR`,\n start,\n end: thickStart,\n refName,\n },\n {\n type: 'CDS',\n start: thickStart,\n end,\n refName,\n },\n )\n } else if (thickStart <= start && thickEnd >= end) {\n // CDS\n subfeatures.push({\n type: 'CDS',\n start,\n end,\n refName,\n })\n } else if (thickStart > start && thickStart < end && thickEnd < end) {\n // UTR | CDS | UTR\n const leftPrime = strand > 0 ? 'five' : 'three'\n const rightPrime = strand > 0 ? 'three' : 'five'\n subfeatures.push(\n {\n type: `${leftPrime}_prime_UTR`,\n start,\n end: thickStart,\n refName,\n },\n {\n type: 'CDS',\n start: thickStart,\n end: thickEnd,\n refName,\n },\n {\n type: `${rightPrime}_prime_UTR`,\n start: thickEnd,\n end,\n refName,\n },\n )\n } else if (thickStart <= start && thickEnd > start && thickEnd < end) {\n // CDS | UTR\n const prime = strand > 0 ? 'three' : 'five'\n subfeatures.push(\n {\n type: 'CDS',\n start,\n end: thickEnd,\n refName,\n },\n {\n type: `${prime}_prime_UTR`,\n start: thickEnd,\n end,\n refName,\n },\n )\n } else if (thickEnd <= start) {\n // right-side UTR\n const prime = strand > 0 ? 'three' : 'five'\n subfeatures.push({\n type: `${prime}_prime_UTR`,\n start,\n end,\n refName,\n })\n }\n })\n\n return { ...rest, strand, type: 'mRNA', refName, subfeatures }\n}\n\nfunction defaultParser(fields: string[], line: string) {\n const obj = Object.fromEntries(\n line.split('\\t').map((f, i) => [fields[i]!, f] as const),\n )\n const {\n blockStarts,\n blockCount,\n chromStarts,\n thickEnd,\n thickStart,\n blockSizes,\n ...rest\n } = obj\n\n return {\n ...rest,\n blockStarts: blockStarts?.split(',').map(r => +r),\n chromStarts: chromStarts?.split(',').map(r => +r),\n blockSizes: blockSizes?.split(',').map(r => +r),\n thickStart: thickStart ? +thickStart : undefined,\n thickEnd: thickEnd ? +thickEnd : undefined,\n blockCount: blockCount ? +blockCount : undefined,\n } as Record<string, unknown>\n}\n\nexport function makeBlocks({\n start,\n uniqueId,\n refName,\n chromStarts,\n blockCount,\n blockSizes,\n blockStarts,\n}: {\n blockCount: number\n start: number\n uniqueId: string\n refName: string\n chromStarts?: number[]\n blockSizes: number[]\n blockStarts?: number[]\n}) {\n const subfeatures = []\n const starts = chromStarts || blockStarts || []\n for (let b = 0; b < blockCount; b++) {\n const bmin = (starts[b] || 0) + start\n const bmax = bmin + (blockSizes[b] || 0)\n subfeatures.push({\n uniqueId: `${uniqueId}-${b}`,\n start: bmin,\n end: bmax,\n refName,\n type: 'block',\n })\n }\n return subfeatures\n}\nexport function featureData(\n line: string,\n colRef: number,\n colStart: number,\n colEnd: number,\n scoreColumn: string,\n parser: BED,\n uniqueId: string,\n names?: string[],\n) {\n const l = line.split('\\t')\n const refName = l[colRef]!\n const start = +l[colStart]!\n const colSame = colStart === colEnd ? 1 : 0\n const end = +l[colEnd]! + colSame\n const data = names\n ? defaultParser(names, line)\n : parser.parseLine(line, { uniqueId })\n\n const {\n blockCount,\n blockSizes,\n blockStarts,\n chromStarts,\n thickStart,\n thickEnd,\n type,\n score,\n chrom: _1,\n chromStart: _2,\n chromEnd: _3,\n ...rest\n } = data\n const subfeatures = blockCount\n ? makeBlocks({\n start,\n uniqueId,\n refName,\n chromStarts,\n blockCount,\n blockSizes,\n blockStarts,\n })\n : []\n const f = {\n ...rest,\n type,\n score: scoreColumn ? +data[scoreColumn] : score,\n start,\n end,\n refName,\n uniqueId,\n subfeatures,\n }\n return new SimpleFeature({\n id: uniqueId,\n data: isUcscProcessedTranscript(data)\n ? ucscProcessedTranscript({\n thickStart: thickStart!,\n thickEnd: thickEnd!,\n blockCount: blockCount!,\n blockSizes: blockSizes!,\n chromStarts: chromStarts,\n ...f,\n })\n : f,\n })\n}\n\nexport function isUcscProcessedTranscript(f: {\n thickStart?: number\n blockCount?: number\n strand?: number\n}) {\n return f.thickStart && f.blockCount && f.strand !== 0\n}\n"],"names":["BedAdapter","BaseFeatureDataAdapter","intervalTrees","loadDataP","opts","pm","this","pluginManager","bedLoc","getConf","buf","openLocation","readFile","buffer","isGzip","unzip","length","Error","lines","TextDecoder","fatal","decode","split","filter","f","headerLines","i","startsWith","push","header","join","features","line","tab","indexOf","refName","slice","autoSql","parser","BED","columnNames","scoreColumn","colRef","colStart","colEnd","loadData","bedFeatures","catch","e","undefined","getRefNames","Object","keys","getHeader","getNames","defline","at","includes","map","field","trim","loadFeatureIntervalTreeHelper","names","intervalTree","IntervalTree","ret","uniqueId","id","featureData","obj","insert","get","loadFeatureIntervalTree","getFeatures","query","ObservableCreate","async","start","end","search","forEach","observer","next","complete","signal","freeResources","ucscProcessedTranscript","feature","subfeatures","oldSubfeatures","thickStart","thickEnd","blockCount","blockSizes","chromStarts","strand","rest","child","type","sort","a","b","block","prime","leftPrime","rightPrime","makeBlocks","blockStarts","starts","bmin","bmax","l","colSame","data","fields","fromEntries","r","defaultParser","parseLine","score","chrom","_1","chromStart","_2","chromEnd","_3","SimpleFeature","isUcscProcessedTranscript"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

annotate x/static/js/4864.28cfc358.chunk.js.map @ 125:49f3d3878413 draft