jbrowse2: x/static/js/7809.eb2c5f08.chunk.js.map comparison

comparison x/static/js/7809.eb2c5f08.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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await updateStatus('Unzipping', statusCallback, () => unzip(buf))\n : buf\n const headerLines = []\n const featureMap = {} as Record<string, string>\n let blockStart = 0\n\n const decoder =\n typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\n let i = 0\n while (blockStart < buffer.length) {\n const n = buffer.indexOf('\\n', blockStart)\n // could be a non-newline ended file, so subarray to end of file if n===-1\n const b =\n n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n)\n const line = (decoder?.decode(b) || b.toString()).trim()\n if (line) {\n if (line.startsWith('#')) {\n headerLines.push(line)\n } else if (line.startsWith('>')) {\n break\n } else {\n const ret = line.indexOf('\\t')\n const refName = line.slice(0, ret)\n if (!featureMap[refName]) {\n featureMap[refName] = ''\n }\n featureMap[refName] += `${line}\\n`\n }\n }\n if (i++ % 10_000 === 0) {\n statusCallback(\n `Loading ${Math.floor(blockStart / 1_000_000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1_000_000).toLocaleString('en-US')} MB`,\n )\n }\n\n blockStart = n + 1\n }\n\n const intervalTreeMap = Object.fromEntries(\n Object.entries(featureMap).map(([refName, lines]) => [\n refName,\n (sc?: (arg: string) => void) => {\n if (!this.calculatedIntervalTreeMap[refName]) {\n sc?.('Parsing GFF data')\n const intervalTree = new IntervalTree()\n parseStringSync(lines)\n .flat()\n .map(\n (f, i) =>\n new SimpleFeature({\n data: featureData(f),\n id: `${this.id}-${refName}-${i}`,\n }),\n )\n .forEach(obj =>\n intervalTree.insert([obj.get('start'), obj.get('end')], obj),\n )\n this.calculatedIntervalTreeMap[refName] = intervalTree\n }\n return this.calculatedIntervalTreeMap[refName]\n },\n ]),\n )\n\n return {\n header: headerLines.join('\\n'),\n intervalTreeMap,\n }\n }\n\n private async loadData(opts: BaseOptions) {\n if (!this.gffFeatures) {\n this.gffFeatures = this.loadDataP(opts).catch((e: unknown) => {\n this.gffFeatures = undefined\n throw e\n })\n }\n\n return this.gffFeatures\n }\n\n public async getRefNames(opts: BaseOptions = {}) {\n const { intervalTreeMap } = await this.loadData(opts)\n return Object.keys(intervalTreeMap)\n }\n\n public async getHeader(opts: BaseOptions = {}) {\n const { header } = await this.loadData(opts)\n return header\n }\n\n public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n try {\n const { start, end, refName } = query\n const { intervalTreeMap } = await this.loadData(opts)\n intervalTreeMap[refName]?.(opts.statusCallback)\n .search([start, end])\n .forEach(f => {\n observer.next(f)\n })\n observer.complete()\n } catch (e) {\n observer.error(e)\n }\n }, opts.signal)\n }\n\n public freeResources(/* { region } */) {}\n}\n","import { GFF3FeatureLineWithRefs } from 'gff-nostream'\n\ninterface GFF3Feature {\n start: number\n end: number\n strand?: number\n type: string | null\n source: string | null\n refName: string\n derived_features: unknown[] | null\n phase?: number\n score?: number\n subfeatures: GFF3Feature[] | undefined\n [key: string]: unknown\n}\n\nexport function featureData(data: GFF3FeatureLineWithRefs): GFF3Feature {\n const {\n end,\n start,\n child_features,\n derived_features,\n attributes,\n type,\n source,\n phase,\n seq_id,\n score,\n strand,\n } = data\n\n let strand2: number | undefined\n if (strand === '+') {\n strand2 = 1\n } else if (strand === '-') {\n strand2 = -1\n } else if (strand === '.') {\n strand2 = 0\n }\n\n const defaultFields = new Set([\n 'start',\n 'end',\n 'seq_id',\n 'score',\n 'type',\n 'source',\n 'phase',\n 'strand',\n ])\n const dataAttributes = attributes || {}\n const resultAttributes = {} as Record<string, unknown>\n for (const a of Object.keys(dataAttributes)) {\n let b = a.toLowerCase()\n if (defaultFields.has(b)) {\n // add \"suffix\" to tag name if it already exists\n // reproduces behavior of NCList\n b += '2'\n }\n if (dataAttributes[a] && a !== '_lineHash') {\n let attr: string | string[] | undefined = dataAttributes[a]\n if (Array.isArray(attr) && attr.length === 1) {\n ;[attr] = attr\n }\n resultAttributes[b] = attr\n }\n }\n\n return {\n ...resultAttributes,\n start: start! - 1,\n end: end!,\n strand: strand2,\n type,\n source,\n refName: seq_id!,\n derived_features,\n phase: phase === null ? 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Mercurial > repos > fubar > jbrowse2

comparison x/static/js/7809.eb2c5f08.chunk.js.map @ 125:49f3d3878413 draft