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

annotate 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

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 {"version":3,"file":"static/js/7809.eb2c5f08.chunk.js","mappings":"4PAkBe,MAAMA,UAAoBC,EAAAA,uBACvCC,0BAA0D,CAAC,EAO3D,eAAcC,CAAUC,GACtB,MAAM,eAAEC,EAAiBA,QAAaD,GAAQ,CAAC,EACzCE,QAAaC,EAAAA,EAAAA,cACjBC,KAAKC,QAAQ,eACbD,KAAKE,eACLC,SAASP,GACLQ,GAASC,EAAAA,EAAAA,QAAOP,SACZQ,EAAAA,EAAAA,cAAa,YAAaT,GAAgB,KAAMU,EAAAA,EAAAA,OAAMT,KAC5DA,EACEU,EAAc,GACdC,EAAa,CAAC,EACpB,IAAIC,EAAa,EAEjB,MAAMC,EACmB,oBAAhBC,YAA8B,IAAIA,YAAY,aAAUC,EAEjE,IAAIC,EAAI,EACR,KAAOJ,EAAaN,EAAOW,QAAQ,CACjC,MAAMC,EAAIZ,EAAOa,QAAQ,KAAMP,GAEzBQ,GACG,IAAPF,EAAWZ,EAAOe,SAAST,GAAcN,EAAOe,SAAST,EAAYM,GACjEI,GAAQT,GAASU,OAAOH,IAAMA,EAAEI,YAAYC,OAClD,GAAIH,EACF,GAAIA,EAAKI,WAAW,KAClBhB,EAAYiB,KAAKL,OACZ,IAAIA,EAAKI,WAAW,KACzB,MACK,CACL,MAAME,EAAMN,EAAKH,QAAQ,MACnBU,EAAUP,EAAKQ,MAAM,EAAGF,GACzBjB,EAAWkB,KACdlB,EAAWkB,GAAW,IAExBlB,EAAWkB,IAAY,GAAGP,KAC5B,EAEEN,IAAM,KAAW,GACnBjB,EACE,WAAWgC,KAAKC,MAAMpB,EAAa,KAAWqB,eAAe,YAAYF,KAAKC,MAAM1B,EAAOW,OAAS,KAAWgB,eAAe,eAIlIrB,EAAaM,EAAI,CACnB,CAEA,MAAMgB,EAAkBC,OAAOC,YAC7BD,OAAOE,QAAQ1B,GAAY2B,KAAI,EAAET,EAASU,KAAW,CACnDV,EACCW,IACC,IAAKtC,KAAKN,0BAA0BiC,GAAU,CAC5CW,IAAK,oBACL,MAAMC,EAAe,IAAIC,EAAAA,IACzBC,EAAAA,EAAAA,GAAgBJ,GACbK,OACAN,KACC,CAACO,EAAG7B,IACF,IAAI8B,EAAAA,EAAc,CAChBC,MAAMC,EAAAA,EAAAA,GAAYH,GAClBI,GAAI,GAAG/C,KAAK+C,MAAMpB,KAAWb,QAGlCkC,SAAQC,GACPV,EAAaW,OAAO,CAACD,EAAIE,IAAI,SAAUF,EAAIE,IAAI,QAASF,KAE5DjD,KAAKN,0BAA0BiC,GAAWY,CAC5C,CACA,OAAOvC,KAAKN,0BAA0BiC,EAAQ,MAKpD,MAAO,CACLyB,OAAQ5C,EAAY6C,KAAK,MACzBrB,kBAEJ,CAEA,cAAcsB,CAAS1D,GAQrB,OAPKI,KAAKuD,cACRvD,KAAKuD,YAAcvD,KAAKL,UAAUC,GAAM4D,OAAOC,IAE7C,MADAzD,KAAKuD,iBAAc1C,EACb4C,CAAC,KAIJzD,KAAKuD,WACd,CAEA,iBAAaG,CAAY9D,EAAoB,CAAC,GAC5C,MAAM,gBAAEoC,SAA0BhC,KAAKsD,SAAS1D,GAChD,OAAOqC,OAAO0B,KAAK3B,EACrB,CAEA,eAAa4B,CAAUhE,EAAoB,CAAC,GAC1C,MAAM,OAAEwD,SAAiBpD,KAAKsD,SAAS1D,GACvC,OAAOwD,CACT,CAEOS,WAAAA,CAAYC,EAAyBlE,EAAoB,CAAC,GAC/D,OAAOmE,EAAAA,EAAAA,mBAA0BC,UAC/B,IACE,MAAM,MAAEC,EAAK,IAAEC,EAAG,QAAEvC,GAAYmC,GAC1B,gBAAE9B,SAA0BhC,KAAKsD,SAAS1D,GAChDoC,EAAgBL,KAAW/B,EAAKC,gBAC7BsE,OAAO,CAACF,EAAOC,IACflB,SAAQL,IACPyB,EAASC,KAAK1B,EAAE,IAEpByB,EAASE,UACX,CAAE,MAAOb,GACPW,EAASG,MAAMd,EACjB,IACC7D,EAAK4E,OACV,CAEOC,aAAAA,GAAiC,E,kBC9HnC,SAAS3B,EAAYD,GAC1B,MAAM,IACJqB,EAAG,MACHD,EAAK,eACLS,EAAc,iBACdC,EAAgB,WAChBC,EAAU,KACVC,EAAI,OACJC,EAAM,MACNC,EAAK,OACLC,EAAM,MACNC,EAAK,OACLC,GACErC,EAEJ,IAAIsC,EACW,MAAXD,EACFC,EAAU,EACU,MAAXD,EACTC,GAAW,EACS,MAAXD,IACTC,EAAU,GAGZ,MAAMC,EAAgB,IAAIC,IAAI,CAC5B,QACA,MACA,SACA,QACA,OACA,SACA,QACA,WAEIC,EAAiBV,GAAc,CAAC,EAChCW,EAAmB,CAAC,EAC1B,IAAK,MAAMC,KAAKvD,OAAO0B,KAAK2B,GAAiB,CAC3C,IAAIpE,EAAIsE,EAAEC,cAMV,GALIL,EAAcM,IAAIxE,KAGpBA,GAAK,KAEHoE,EAAeE,IAAY,cAANA,EAAmB,CAC1C,IAAIG,EAAsCL,EAAeE,GACrDI,MAAMC,QAAQF,IAAyB,IAAhBA,EAAK5E,UAC5B4E,GAAQA,GAEZJ,EAAiBrE,GAAKyE,CACxB,CACF,CAEA,MAAO,IACFJ,EACHtB,MAAOA,EAAS,EAChBC,IAAKA,EACLgB,OAAQC,EACRN,OACAC,SACAnD,QAASqD,EACTL,mBACAI,MAAiB,OAAVA,OAAiBlE,EAAYiF,OAAOf,GAC3CE,MAAiB,OAAVA,OAAiBpE,EAAYoE,EACpCc,YAAarB,EAAesB,SAAQC,GAClCA,EAAU7D,KAAI8D,GAAYpD,EAAYoD,OAG5C,C","sources":["../../../plugins/gff3/src/Gff3Adapter/Gff3Adapter.ts","../../../plugins/gff3/src/featureData.ts"],"sourcesContent":["import {\n BaseFeatureDataAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { NoAssemblyRegion } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport IntervalTree from '@flatten-js/interval-tree'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { parseStringSync } from 'gff-nostream'\nimport { isGzip, updateStatus } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n\nimport { featureData } from '../featureData'\n\ntype StatusCallback = (arg: string) => void\n\nexport default class Gff3Adapter extends BaseFeatureDataAdapter {\n calculatedIntervalTreeMap: Record<string, IntervalTree> = {}\n\n gffFeatures?: Promise<{\n header: string\n intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>\n }>\n\n private async loadDataP(opts?: BaseOptions) {\n const { statusCallback = () => {} } = opts \|\| {}\n const buf = (await openLocation(\n this.getConf('gffLocation'),\n this.pluginManager,\n ).readFile(opts)) as Buffer\n const buffer = isGzip(buf)\n ? 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rev

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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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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

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