jbrowse2: x/static/js/4234.63e1ba57.chunk.js.map comparison

comparison x/static/js/4234.63e1ba57.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
	1 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{ BigWig } from '@gmod/bbi'\nimport {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { updateStatus, Feature } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport {\n rectifyStats,\n UnrectifiedQuantitativeStats,\n} from '@jbrowse/core/util/stats'\n\ninterface WiggleOptions extends BaseOptions {\n resolution?: number\n}\n\nexport default class BigWigAdapter extends BaseFeatureDataAdapter {\n private setupP?: Promise<{\n bigwig: BigWig\n header: Awaited<ReturnType<BigWig['getHeader']>>\n }>\n\n public static capabilities = [\n 'hasResolution',\n 'hasLocalStats',\n 'hasGlobalStats',\n ]\n\n private async setupPre(opts?: BaseOptions) {\n const { statusCallback = () => {} } = opts \|\| {}\n const pm = this.pluginManager\n const bigwig = new BigWig({\n filehandle: openLocation(this.getConf('bigWigLocation'), pm),\n })\n const header = await updateStatus(\n 'Downloading bigwig header',\n statusCallback,\n () => bigwig.getHeader(opts),\n )\n return { bigwig, header }\n }\n\n async setup(opts?: BaseOptions) {\n if (!this.setupP) {\n this.setupP = this.setupPre(opts).catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n public async getRefNames(opts?: BaseOptions) {\n const { header } = await this.setup(opts)\n return Object.keys(header.refsByName)\n }\n\n public async refIdToName(refId: number) {\n const { header } = await this.setup()\n return header.refsByNumber[refId]?.name\n }\n\n public async getGlobalStats(opts?: BaseOptions) {\n const { header } = await this.setup(opts)\n return rectifyStats(header.totalSummary as UnrectifiedQuantitativeStats)\n }\n\n public getFeatures(region: Region, opts: WiggleOptions = {}) {\n const { refName, start, end } = region\n const {\n bpPerPx = 0,\n signal,\n resolution = 1,\n statusCallback = () => {},\n } = opts\n return ObservableCreate<Feature>(async observer => {\n statusCallback('Downloading bigwig data')\n const source = this.getConf('source')\n const { bigwig } = await this.setup(opts)\n const feats = await bigwig.getFeatures(refName, start, end, {\n ...opts,\n basesPerSpan: bpPerPx / resolution,\n })\n\n for (const data of feats) {\n if (source) {\n // @ts-expect-error\n data.source = source\n }\n const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`\n // @ts-expect-error\n data.refName = refName\n data.uniqueId = uniqueId\n observer.next({\n // @ts-expect-error\n get: (str: string) => (data as Record<string, unknown>)[str],\n id: () => uniqueId,\n // @ts-expect-error\n toJSON: () => data,\n })\n }\n observer.complete()\n }, signal)\n }\n\n // always render bigwig instead of calculating a feature density for it\n async getMultiRegionFeatureDensityStats(_regions: Region[]) {\n return { featureDensity: 0 }\n }\n\n 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1 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{ BigWig } from '@gmod/bbi'\nimport {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { updateStatus, Feature } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport {\n rectifyStats,\n UnrectifiedQuantitativeStats,\n} from '@jbrowse/core/util/stats'\n\ninterface WiggleOptions extends BaseOptions {\n resolution?: number\n}\n\nexport default class BigWigAdapter extends BaseFeatureDataAdapter {\n private setupP?: Promise<{\n bigwig: BigWig\n header: Awaited<ReturnType<BigWig['getHeader']>>\n }>\n\n public static capabilities = [\n 'hasResolution',\n 'hasLocalStats',\n 'hasGlobalStats',\n ]\n\n private async setupPre(opts?: BaseOptions) {\n const { statusCallback = () => {} } = opts || {}\n const pm = this.pluginManager\n const bigwig = new BigWig({\n filehandle: openLocation(this.getConf('bigWigLocation'), pm),\n })\n const header = await updateStatus(\n 'Downloading bigwig header',\n statusCallback,\n () => bigwig.getHeader(opts),\n )\n return { bigwig, header }\n }\n\n async setup(opts?: BaseOptions) {\n if (!this.setupP) {\n this.setupP = this.setupPre(opts).catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n public async getRefNames(opts?: BaseOptions) {\n const { header } = await this.setup(opts)\n return Object.keys(header.refsByName)\n }\n\n public async refIdToName(refId: number) {\n const { header } = await this.setup()\n return header.refsByNumber[refId]?.name\n }\n\n public async getGlobalStats(opts?: BaseOptions) {\n const { header } = await this.setup(opts)\n return rectifyStats(header.totalSummary as UnrectifiedQuantitativeStats)\n }\n\n public getFeatures(region: Region, opts: WiggleOptions = {}) {\n const { refName, start, end } = region\n const {\n bpPerPx = 0,\n signal,\n resolution = 1,\n statusCallback = () => {},\n } = opts\n return ObservableCreate<Feature>(async observer => {\n statusCallback('Downloading bigwig data')\n const source = this.getConf('source')\n const { bigwig } = await this.setup(opts)\n const feats = await bigwig.getFeatures(refName, start, end, {\n ...opts,\n basesPerSpan: bpPerPx / resolution,\n })\n\n for (const data of feats) {\n if (source) {\n // @ts-expect-error\n data.source = source\n }\n const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`\n // @ts-expect-error\n data.refName = refName\n data.uniqueId = uniqueId\n observer.next({\n // @ts-expect-error\n get: (str: string) => (data as Record<string, unknown>)[str],\n id: () => uniqueId,\n // @ts-expect-error\n toJSON: () => data,\n })\n }\n observer.complete()\n }, signal)\n }\n\n // always render bigwig instead of calculating a feature density for it\n async getMultiRegionFeatureDensityStats(_regions: Region[]) {\n return { featureDensity: 0 }\n }\n\n public freeResources(): void {}\n}\n"],"names":["BigWigAdapter","BaseFeatureDataAdapter","setupPre","opts","statusCallback","pm","this","pluginManager","bigwig","BigWig","filehandle","openLocation","getConf","header","updateStatus","getHeader","setup","setupP","catch","e","undefined","getRefNames","Object","keys","refsByName","refIdToName","refId","refsByNumber","name","getGlobalStats","rectifyStats","totalSummary","getFeatures","region","refName","start","end","bpPerPx","signal","resolution","ObservableCreate","async","source","feats","basesPerSpan","data","uniqueId","observer","next","get","str","id","toJSON","complete","getMultiRegionFeatureDensityStats","_regions","featureDensity","freeResources"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

comparison x/static/js/4234.63e1ba57.chunk.js.map @ 125:49f3d3878413 draft