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

annotate 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

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 { doesIntersect2 } from '@jbrowse/core/util/range'\nimport { Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport { parseStringSync } from 'gff-nostream'\nimport { Observer } from 'rxjs'\nimport {\n readConfObject,\n AnyConfigurationModel,\n} from '@jbrowse/core/configuration'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport { featureData } from '../featureData'\n\ninterface LineFeature {\n start: number\n end: number\n lineHash: number\n fields: string[]\n}\n\nexport default class Gff3TabixAdapter extends BaseFeatureDataAdapter {\n protected gff: TabixIndexedFile\n\n protected dontRedispatch: string[]\n\n public constructor(\n config: AnyConfigurationModel,\n getSubAdapter?: getSubAdapterType,\n pluginManager?: PluginManager,\n ) {\n super(config, getSubAdapter, pluginManager)\n const gffGzLocation = readConfObject(config, 'gffGzLocation')\n const indexType = readConfObject(config, ['index', 'indexType'])\n const location = readConfObject(config, ['index', 'location'])\n const dontRedispatch = readConfObject(config, 'dontRedispatch')\n\n this.dontRedispatch = dontRedispatch \|\| ['chromosome', 'contig', 'region']\n this.gff = new TabixIndexedFile({\n filehandle: openLocation(gffGzLocation, this.pluginManager),\n csiFilehandle:\n indexType === 'CSI'\n ? 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: 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{\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 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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

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Mercurial > repos > fubar > jbrowse2

annotate x/static/js/7409.8e71acc1.chunk.js.map @ 125:49f3d3878413 draft