jbrowse2: x/static/js/3167.312d0953.chunk.js.map annotate

annotate x/static/js/3167.312d0953.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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Region[] } = {}) {\n const r1 = opts.regions?.[0]?.assemblyName\n if (!r1) {\n throw new Error('no assembly name provided')\n }\n\n const idx = this.getAssemblyNames().indexOf(r1)\n const names = await this.pif.getReferenceSequenceNames(opts)\n if (idx === 0) {\n return names.filter(n => n.startsWith('q')).map(n => n.slice(1))\n } else if (idx === 1) {\n return names.filter(n => n.startsWith('t')).map(n => n.slice(1))\n } else {\n return []\n }\n }\n\n getFeatures(query: Region, opts: PAFOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { assemblyName } = query\n\n const assemblyNames = this.getAssemblyNames()\n const index = assemblyNames.indexOf(assemblyName)\n const flip = index === 0\n const letter = flip ? 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-1 : 1,\n },\n ]\n }),\n )\n}\n\nexport async function readFile(file: GenericFilehandle, opts?: BaseOptions) {\n const buffer = (await file.readFile(opts)) as Buffer\n return new TextDecoder('utf8', { fatal: true }).decode(\n isGzip(buffer) ? await unzip(buffer) : buffer,\n )\n}\n\nexport function zip(a: number[], b: number[]) {\n return a.map((e, i) => [e, b[i]] as [number, number])\n}\n\nconst decoder =\n typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\nexport function parseLineByLine(\n buffer: Buffer,\n cb: (line: string) => PAFRecord,\n) {\n let blockStart = 0\n const entries = []\n while (blockStart < buffer.length) {\n const n = buffer.indexOf('\\n', blockStart)\n if (n === -1) {\n break\n }\n const b = buffer.subarray(blockStart, n)\n const line = (decoder?.decode(b) \|\| b.toString()).trim()\n if (line) {\n entries.push(cb(line))\n }\n\n blockStart = n + 1\n }\n return entries\n}\n\nexport function parsePAFLine(line: string) {\n const [\n qname,\n ,\n qstart,\n qend,\n strand,\n tname,\n ,\n tstart,\n tend,\n numMatches,\n blockLen,\n mappingQual,\n ...fields\n ] = line.split('\\t')\n\n const rest = Object.fromEntries(\n fields.map(field => {\n const r = field.indexOf(':')\n const fieldName = field.slice(0, r)\n const fieldValue = field.slice(r + 3)\n return [fieldName, fieldValue]\n }),\n )\n\n return {\n tname,\n tstart: +tstart!,\n tend: +tend!,\n qname,\n qstart: +qstart!,\n qend: +qend!,\n strand: strand === '-' ? 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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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{\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { FileLocation, Region } from '@jbrowse/core/util/types'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { TabixIndexedFile } from '@gmod/tabix'\n\n// locals\nimport { parsePAFLine } from '../util'\nimport SyntenyFeature from '../SyntenyFeature'\n\ninterface PAFOptions extends BaseOptions {\n config?: AnyConfigurationModel\n}\n\nexport default class PAFAdapter extends BaseFeatureDataAdapter {\n public static capabilities = ['getFeatures', 'getRefNames']\n\n protected pif: TabixIndexedFile\n\n public constructor(\n config: AnyConfigurationModel,\n getSubAdapter?: getSubAdapterType,\n pluginManager?: PluginManager,\n ) {\n super(config, getSubAdapter, pluginManager)\n const pifGzLoc = this.getConf('pifGzLocation') as FileLocation\n const type = this.getConf(['index', 'indexType'])\n const loc = this.getConf(['index', 'location'])\n const pm = this.pluginManager\n\n this.pif = new TabixIndexedFile({\n filehandle: openLocation(pifGzLoc, pm),\n csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,\n tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,\n chunkCacheSize: 50 * 2 ** 20,\n })\n }\n async getHeader() {\n return this.pif.getHeader()\n }\n\n getAssemblyNames(): string[] {\n const assemblyNames = this.getConf('assemblyNames') as string[]\n if (assemblyNames.length === 0) {\n return [\n this.getConf('queryAssembly') as string,\n this.getConf('targetAssembly') as string,\n ]\n }\n return assemblyNames\n }\n\n public async hasDataForRefName() {\n return true\n }\n\n async getRefNames(opts: BaseOptions & { regions?: Region[] } = {}) {\n const r1 = opts.regions?.[0]?.assemblyName\n if (!r1) {\n throw new Error('no assembly name provided')\n }\n\n const idx = this.getAssemblyNames().indexOf(r1)\n const names = await this.pif.getReferenceSequenceNames(opts)\n if (idx === 0) {\n return names.filter(n => n.startsWith('q')).map(n => n.slice(1))\n } else if (idx === 1) {\n return names.filter(n => n.startsWith('t')).map(n => n.slice(1))\n } else {\n return []\n }\n }\n\n getFeatures(query: Region, opts: PAFOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const { assemblyName } = query\n\n const assemblyNames = this.getAssemblyNames()\n const index = assemblyNames.indexOf(assemblyName)\n const flip = index === 0\n const letter = flip ? 'q' : 't'\n\n await this.pif.getLines(letter + query.refName, query.start, query.end, {\n lineCallback: (line, fileOffset) => {\n const r = parsePAFLine(line)\n const refName = r.qname.slice(1)\n const start = r.qstart\n const end = r.qend\n const mateName = r.tname\n const mateStart = r.tstart\n const mateEnd = r.tend\n\n const { extra, strand } = r\n const { numMatches = 0, blockLen = 1, cg, ...rest } = extra\n\n observer.next(\n new SyntenyFeature({\n uniqueId: fileOffset + assemblyName,\n assemblyName,\n start,\n end,\n type: 'match',\n refName,\n strand,\n ...rest,\n CIGAR: extra.cg,\n syntenyId: fileOffset,\n identity: numMatches / blockLen,\n numMatches,\n blockLen,\n mate: {\n start: mateStart,\n end: mateEnd,\n refName: mateName,\n assemblyName: assemblyNames[+flip],\n },\n }),\n )\n },\n signal: opts.signal,\n })\n\n observer.complete()\n })\n }\n\n freeResources(/* { query } */): void {}\n}\n","import { SimpleFeature } from '@jbrowse/core/util'\nimport { MismatchParser } from '@jbrowse/plugin-alignments'\n\n// locals\nconst { getMismatches } = MismatchParser\n\nexport default class SyntenyFeature extends SimpleFeature {\n get(arg: string): any {\n if (arg === 'mismatches') {\n return getMismatches(this.get('CIGAR'))\n }\n return super.get(arg)\n }\n}\n","import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { isGzip } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n\nimport { PAFRecord } from './PAFAdapter/util'\n\nexport function parseBed(text: string) {\n return new Map(\n text\n .split(/\\n|\\r\\n|\\r/)\n .filter(f => !!f || f.startsWith('#'))\n .map(line => {\n const [refName, start, end, name, score, strand] = line.split('\\t')\n return [\n name,\n {\n refName,\n start: +start!,\n end: +end!,\n score: +score!,\n name,\n strand: strand === '-' ? -1 : 1,\n },\n ]\n }),\n )\n}\n\nexport async function readFile(file: GenericFilehandle, opts?: BaseOptions) {\n const buffer = (await file.readFile(opts)) as Buffer\n return new TextDecoder('utf8', { fatal: true }).decode(\n isGzip(buffer) ? await unzip(buffer) : buffer,\n )\n}\n\nexport function zip(a: number[], b: number[]) {\n return a.map((e, i) => [e, b[i]] as [number, number])\n}\n\nconst decoder =\n typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\nexport function parseLineByLine(\n buffer: Buffer,\n cb: (line: string) => PAFRecord,\n) {\n let blockStart = 0\n const entries = []\n while (blockStart < buffer.length) {\n const n = buffer.indexOf('\\n', blockStart)\n if (n === -1) {\n break\n }\n const b = buffer.subarray(blockStart, n)\n const line = (decoder?.decode(b) || b.toString()).trim()\n if (line) {\n entries.push(cb(line))\n }\n\n blockStart = n + 1\n }\n return entries\n}\n\nexport function parsePAFLine(line: string) {\n const [\n qname,\n ,\n qstart,\n qend,\n strand,\n tname,\n ,\n tstart,\n tend,\n numMatches,\n blockLen,\n mappingQual,\n ...fields\n ] = line.split('\\t')\n\n const rest = Object.fromEntries(\n fields.map(field => {\n const r = field.indexOf(':')\n const fieldName = field.slice(0, r)\n const fieldValue = field.slice(r + 3)\n return [fieldName, fieldValue]\n }),\n )\n\n return {\n tname,\n tstart: +tstart!,\n tend: +tend!,\n qname,\n qstart: +qstart!,\n qend: +qend!,\n strand: strand === '-' ? -1 : 1,\n extra: {\n numMatches: +numMatches!,\n blockLen: +blockLen!,\n mappingQual: +mappingQual!,\n ...rest,\n },\n } as PAFRecord\n}\n\nexport function flipCigar(cigar: string[]) {\n const arr = []\n for (let i = cigar.length - 2; i >= 0; i -= 2) {\n arr.push(cigar[i])\n const op = cigar[i + 1]\n if (op === 'D') {\n arr.push('I')\n } else if (op === 'I') {\n arr.push('D')\n } else {\n arr.push(op)\n }\n }\n return arr\n}\n\nexport function swapIndelCigar(cigar: string) {\n return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')\n}\n"],"names":["PAFAdapter","BaseFeatureDataAdapter","constructor","config","getSubAdapter","pluginManager","super","pifGzLoc","this","getConf","type","loc","pm","pif","TabixIndexedFile","filehandle","openLocation","csiFilehandle","undefined","tbiFilehandle","chunkCacheSize","getHeader","getAssemblyNames","assemblyNames","length","hasDataForRefName","getRefNames","opts","r1","regions","assemblyName","Error","idx","indexOf","names","getReferenceSequenceNames","filter","n","startsWith","map","slice","getFeatures","query","ObservableCreate","async","flip","letter","getLines","refName","start","end","lineCallback","line","fileOffset","r","parsePAFLine","qname","qstart","qend","mateName","tname","mateStart","tstart","mateEnd","tend","extra","strand","numMatches","blockLen","cg","rest","observer","next","SyntenyFeature","uniqueId","CIGAR","syntenyId","identity","mate","signal","complete","freeResources","getMismatches","MismatchParser","SimpleFeature","get","arg","parseBed","text","Map","split","f","name","score","readFile","file","buffer","TextDecoder","fatal","decode","isGzip","unzip","zip","a","b","e","i","decoder","parseLineByLine","cb","blockStart","entries","subarray","toString","trim","push","mappingQual","fields","Object","fromEntries","field","flipCigar","cigar","arr","op","swapIndelCigar","replaceAll"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

annotate x/static/js/3167.312d0953.chunk.js.map @ 125:49f3d3878413 draft