jbrowse2: x/static/js/7409.8e71acc1.chunk.js.map comparison

comparison x/static/js/7409.8e71acc1.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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openLocation(location, this.pluginManager)\n : undefined,\n tbiFilehandle:\n indexType !== 'CSI'\n ? openLocation(location, this.pluginManager)\n : undefined,\n chunkCacheSize: 50 * 2 ** 20,\n renameRefSeqs: (n: string) => n,\n })\n }\n\n public async getRefNames(opts: BaseOptions = {}) {\n return this.gff.getReferenceSequenceNames(opts)\n }\n\n public async getHeader() {\n return this.gff.getHeader()\n }\n\n public getFeatures(query: Region, opts: BaseOptions = {}) {\n return ObservableCreate<Feature>(async observer => {\n const metadata = await this.gff.getMetadata()\n await this.getFeaturesHelper(query, opts, metadata, observer, true)\n }, opts.signal)\n }\n\n private async getFeaturesHelper(\n query: Region,\n opts: BaseOptions,\n metadata: { columnNumbers: { start: number; end: number } },\n observer: Observer<Feature>,\n allowRedispatch: boolean,\n originalQuery = query,\n ) {\n try {\n const lines: LineFeature[] = []\n\n await this.gff.getLines(\n query.refName,\n query.start,\n query.end,\n (line, fileOffset) => {\n lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset))\n },\n )\n if (allowRedispatch && lines.length) {\n let minStart = Number.POSITIVE_INFINITY\n let maxEnd = Number.NEGATIVE_INFINITY\n for (const line of lines) {\n const featureType = line.fields[2]!\n // only expand redispatch range if feature is not a \"dontRedispatch\"\n // type skips large regions like chromosome,region\n if (!this.dontRedispatch.includes(featureType)) {\n const start = line.start - 1 // gff is 1-based\n if (start < minStart) {\n minStart = start\n }\n if (line.end > maxEnd) {\n maxEnd = line.end\n }\n }\n }\n if (maxEnd > query.end \|\| minStart < query.start) {\n // make a new feature callback to only return top-level features\n // in the original query range\n await this.getFeaturesHelper(\n { ...query, start: minStart, end: maxEnd },\n opts,\n metadata,\n observer,\n false,\n query,\n )\n return\n }\n }\n\n const gff3 = lines\n .map(lineRecord => {\n if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {\n if (!lineRecord.fields[8].includes('_lineHash')) {\n lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`\n }\n } else {\n lineRecord.fields[8] = `_lineHash=${lineRecord.lineHash}`\n }\n return lineRecord.fields.join('\\t')\n })\n .join('\\n')\n\n for (const featureLocs of parseStringSync(gff3)) {\n for (const featureLoc of featureLocs) {\n const f = new SimpleFeature({\n data: featureData(featureLoc),\n id: `${this.id}-offset-${featureLoc.attributes?._lineHash?.[0]}`,\n })\n if (\n doesIntersect2(\n f.get('start'),\n f.get('end'),\n originalQuery.start,\n originalQuery.end,\n )\n ) {\n observer.next(f)\n }\n }\n }\n observer.complete()\n } catch (e) {\n observer.error(e)\n }\n }\n\n private parseLine(\n columnNumbers: { start: number; end: number },\n line: string,\n fileOffset: number,\n ) {\n const fields = line.split('\\t')\n\n // note: index column numbers are 1-based\n return {\n start: +fields[columnNumbers.start - 1]!,\n end: +fields[columnNumbers.end - 1]!,\n lineHash: fileOffset,\n fields,\n }\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/7409.8e71acc1.chunk.js.map @ 125:49f3d3878413 draft