jbrowse2: x/static/js/6214.0ed0ac32.chunk.js.map comparison

comparison x/static/js/6214.0ed0ac32.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

comparison

equal deleted inserted replaced

124:137e08517410	125:49f3d3878413
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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 { FileLocation, Region, Feature } from '@jbrowse/core/util'\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\n// locals\nimport { featureData } from '../util'\n\nexport default class BedTabixAdapter extends BaseFeatureDataAdapter {\n private parser: BED\n\n protected bed: TabixIndexedFile\n\n protected columnNames: string[]\n\n protected scoreColumn: string\n\n public static capabilities = ['getFeatures', 'getRefNames']\n\n public constructor(\n config: AnyConfigurationModel,\n getSubAdapter?: getSubAdapterType,\n pluginManager?: PluginManager,\n ) {\n super(config, getSubAdapter, pluginManager)\n const bedGzLoc = this.getConf('bedGzLocation') as FileLocation\n const type = this.getConf(['index', 'indexType'])\n const loc = this.getConf(['index', 'location'])\n const autoSql = this.getConf('autoSql')\n const pm = this.pluginManager\n\n this.bed = new TabixIndexedFile({\n filehandle: openLocation(bedGzLoc, pm),\n csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,\n tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,\n chunkCacheSize: 50 * 2 ** 20,\n })\n this.columnNames = this.getConf('columnNames')\n this.scoreColumn = this.getConf('scoreColumn')\n this.parser = new BED({ autoSql })\n }\n\n public async getRefNames(opts: BaseOptions = {}) {\n return this.bed.getReferenceSequenceNames(opts)\n }\n\n async getHeader() {\n return this.bed.getHeader()\n }\n\n async getNames() {\n if (this.columnNames.length) {\n return this.columnNames\n }\n const header = await this.bed.getHeader()\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(f => f.trim())\n : undefined\n }\n\n public getFeatures(query: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const meta = await this.bed.getMetadata()\n const { columnNumbers } = meta\n const colRef = columnNumbers.ref - 1\n const colStart = columnNumbers.start - 1\n const colEnd = columnNumbers.end - 1\n // colSame handles special case for tabix where a single column is both\n // the start and end, this is assumed to be covering the base at this\n // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same\n const names = await this.getNames()\n await this.bed.getLines(query.refName, query.start, query.end, {\n lineCallback: (line, fileOffset) => {\n observer.next(\n featureData(\n line,\n colRef,\n colStart,\n colEnd,\n this.scoreColumn,\n this.parser,\n `${this.id}-${fileOffset}`,\n names,\n ),\n )\n },\n signal: opts.signal,\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":["BedTabixAdapter","BaseFeatureDataAdapter","constructor","config","getSubAdapter","pluginManager","super","bedGzLoc","this","getConf","type","loc","autoSql","pm","bed","TabixIndexedFile","filehandle","openLocation","csiFilehandle","undefined","tbiFilehandle","chunkCacheSize","columnNames","scoreColumn","parser","BED","getRefNames","opts","getReferenceSequenceNames","getHeader","getNames","length","defline","split","filter","f","at","includes","slice","map","trim","getFeatures","query","ObservableCreate","async","meta","getMetadata","columnNumbers","colRef","ref","colStart","start","colEnd","end","names","getLines","refName","lineCallback","line","fileOffset","observer","next","featureData","id","signal","complete","freeResources","ucscProcessedTranscript","feature","subfeatures","oldSubfeatures","thickStart","thickEnd","blockCount","blockSizes","chromStarts","strand","rest","child","sort","a","b","forEach","block","prime","push","leftPrime","rightPrime","makeBlocks","uniqueId","blockStarts","starts","bmin","bmax","l","colSame","data","fields","obj","Object","fromEntries","i","r","defaultParser","parseLine","score","chrom","_1","chromStart","_2","chromEnd","_3","SimpleFeature","isUcscProcessedTranscript"],"sourceRoot":""}

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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 { FileLocation, Region, Feature } from '@jbrowse/core/util'\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\n// locals\nimport { featureData } from '../util'\n\nexport default class BedTabixAdapter extends BaseFeatureDataAdapter {\n private parser: BED\n\n protected bed: TabixIndexedFile\n\n protected columnNames: string[]\n\n protected scoreColumn: string\n\n public static capabilities = ['getFeatures', 'getRefNames']\n\n public constructor(\n config: AnyConfigurationModel,\n getSubAdapter?: getSubAdapterType,\n pluginManager?: PluginManager,\n ) {\n super(config, getSubAdapter, pluginManager)\n const bedGzLoc = this.getConf('bedGzLocation') as FileLocation\n const type = this.getConf(['index', 'indexType'])\n const loc = this.getConf(['index', 'location'])\n const autoSql = this.getConf('autoSql')\n const pm = this.pluginManager\n\n this.bed = new TabixIndexedFile({\n filehandle: openLocation(bedGzLoc, pm),\n csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,\n tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,\n chunkCacheSize: 50 * 2 ** 20,\n })\n this.columnNames = this.getConf('columnNames')\n this.scoreColumn = this.getConf('scoreColumn')\n this.parser = new BED({ autoSql })\n }\n\n public async getRefNames(opts: BaseOptions = {}) {\n return this.bed.getReferenceSequenceNames(opts)\n }\n\n async getHeader() {\n return this.bed.getHeader()\n }\n\n async getNames() {\n if (this.columnNames.length) {\n return this.columnNames\n }\n const header = await this.bed.getHeader()\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(f => f.trim())\n : undefined\n }\n\n public getFeatures(query: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const meta = await this.bed.getMetadata()\n const { columnNumbers } = meta\n const colRef = columnNumbers.ref - 1\n const colStart = columnNumbers.start - 1\n const colEnd = columnNumbers.end - 1\n // colSame handles special case for tabix where a single column is both\n // the start and end, this is assumed to be covering the base at this\n // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same\n const names = await this.getNames()\n await this.bed.getLines(query.refName, query.start, query.end, {\n lineCallback: (line, fileOffset) => {\n observer.next(\n featureData(\n line,\n colRef,\n colStart,\n colEnd,\n this.scoreColumn,\n this.parser,\n `${this.id}-${fileOffset}`,\n names,\n ),\n )\n },\n signal: opts.signal,\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":["BedTabixAdapter","BaseFeatureDataAdapter","constructor","config","getSubAdapter","pluginManager","super","bedGzLoc","this","getConf","type","loc","autoSql","pm","bed","TabixIndexedFile","filehandle","openLocation","csiFilehandle","undefined","tbiFilehandle","chunkCacheSize","columnNames","scoreColumn","parser","BED","getRefNames","opts","getReferenceSequenceNames","getHeader","getNames","length","defline","split","filter","f","at","includes","slice","map","trim","getFeatures","query","ObservableCreate","async","meta","getMetadata","columnNumbers","colRef","ref","colStart","start","colEnd","end","names","getLines","refName","lineCallback","line","fileOffset","observer","next","featureData","id","signal","complete","freeResources","ucscProcessedTranscript","feature","subfeatures","oldSubfeatures","thickStart","thickEnd","blockCount","blockSizes","chromStarts","strand","rest","child","sort","a","b","forEach","block","prime","push","leftPrime","rightPrime","makeBlocks","uniqueId","blockStarts","starts","bmin","bmax","l","colSame","data","fields","obj","Object","fromEntries","i","r","defaultParser","parseLine","score","chrom","_1","chromStart","_2","chromEnd","_3","SimpleFeature","isUcscProcessedTranscript"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

comparison x/static/js/6214.0ed0ac32.chunk.js.map @ 125:49f3d3878413 draft