--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/x/static/js/4864.28cfc358.chunk.js.map	Sat Oct 05 23:58:05 2024 +0000
@@ -0,0 +1,1 @@
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BED from '@gmod/bed'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Region, Feature, isGzip } from '@jbrowse/core/util'\nimport IntervalTree from '@flatten-js/interval-tree'\nimport { unzip } from '@gmod/bgzf-filehandle'\n\n// locals\nimport { featureData } from '../util'\n\nexport default class BedAdapter extends BaseFeatureDataAdapter {\n  protected bedFeatures?: Promise<{\n    header: string\n    features: Record<string, string[]>\n    parser: BED\n    columnNames: string[]\n    scoreColumn: string\n    colRef: number\n    colStart: number\n    colEnd: number\n  }>\n\n  protected intervalTrees: Record<\n    string,\n    Promise<IntervalTree | undefined> | undefined\n  > = {}\n\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private async loadDataP(opts: BaseOptions = {}) {\n    const pm = this.pluginManager\n    const bedLoc = this.getConf('bedLocation')\n    const buf = await openLocation(bedLoc, pm).readFile(opts)\n    const buffer = isGzip(buf) ? await unzip(buf) : buf\n    // 512MB  max chrome string length is 512MB\n    if (buffer.length > 536_870_888) {\n      throw new Error('Data exceeds maximum string length (512MB)')\n    }\n    const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)\n    const lines = data.split(/\\n|\\r\\n|\\r/).filter(f => !!f)\n    const headerLines = []\n    let i = 0\n    for (; i < lines.length && lines[i]!.startsWith('#'); i++) {\n      headerLines.push(lines[i])\n    }\n    const header = headerLines.join('\\n')\n    const features = {} as Record<string, string[]>\n    for (; i < lines.length; i++) {\n      const line = lines[i]!\n      const tab = line.indexOf('\\t')\n      const refName = line.slice(0, tab)\n      if (!features[refName]) {\n        features[refName] = []\n      }\n      features[refName].push(line)\n    }\n\n    const autoSql = this.getConf('autoSql') as string\n    const parser = new BED({ autoSql })\n    const columnNames = this.getConf('columnNames')\n    const scoreColumn = this.getConf('scoreColumn')\n    const colRef = this.getConf('colRef')\n    const colStart = this.getConf('colStart')\n    const colEnd = this.getConf('colEnd')\n\n    return {\n      header,\n      features,\n      parser,\n      columnNames,\n      scoreColumn,\n      colRef,\n      colStart,\n      colEnd,\n    }\n  }\n\n  private async loadData(opts: BaseOptions = {}) {\n    if (!this.bedFeatures) {\n      this.bedFeatures = this.loadDataP(opts).catch((e: unknown) => {\n        this.bedFeatures = undefined\n        throw e\n      })\n    }\n\n    return this.bedFeatures\n  }\n\n  public async getRefNames(opts: BaseOptions = {}) {\n    const { features } = await this.loadData(opts)\n    return Object.keys(features)\n  }\n\n  async getHeader(opts: BaseOptions = {}) {\n    const { header } = await this.loadData(opts)\n    return header\n  }\n\n  async getNames() {\n    const { header, columnNames } = await this.loadData()\n    if (columnNames.length) {\n      return columnNames\n    }\n    const defs = header.split(/\\n|\\r\\n|\\r/).filter(f => !!f)\n    const defline = defs.at(-1)\n    return defline?.includes('\\t')\n      ? defline\n          .slice(1)\n          .split('\\t')\n          .map(field => field.trim())\n      : undefined\n  }\n\n  private async loadFeatureIntervalTreeHelper(refName: string) {\n    const { colRef, colStart, colEnd, features, parser, scoreColumn } =\n      await this.loadData()\n    const lines = features[refName]\n    if (!lines) {\n      return undefined\n    }\n    const names = await this.getNames()\n\n    const intervalTree = new IntervalTree()\n    const ret = lines.map((f, i) => {\n      const uniqueId = `${this.id}-${refName}-${i}`\n      return featureData(\n        f,\n        colRef,\n        colStart,\n        colEnd,\n        scoreColumn,\n        parser,\n        uniqueId,\n        names,\n      )\n    })\n\n    for (const obj of ret) {\n      intervalTree.insert([obj.get('start'), obj.get('end')], obj)\n    }\n    return intervalTree\n  }\n\n  private async loadFeatureIntervalTree(refName: string) {\n    if (!this.intervalTrees[refName]) {\n      this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(\n        refName,\n      ).catch((e: unknown) => {\n        this.intervalTrees[refName] = undefined\n        throw e\n      })\n    }\n    return this.intervalTrees[refName]\n  }\n\n  public getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { start, end, refName } = query\n      const intervalTree = await this.loadFeatureIntervalTree(refName)\n      intervalTree?.search([start, end]).forEach(f => {\n        observer.next(f)\n      })\n      observer.complete()\n    }, opts.signal)\n  }\n\n  public freeResources(): void {}\n}\n","import BED from '@gmod/bed'\nimport { SimpleFeature } from '@jbrowse/core/util'\n\nexport interface MinimalFeature {\n  type: string\n  start: number\n  end: number\n  refName: string\n  [key: string]: unknown\n}\nexport interface TranscriptFeat extends MinimalFeature {\n  thickStart: number\n  thickEnd: number\n  blockCount: number\n  blockSizes: number[]\n  chromStarts: number[]\n  refName: string\n  strand?: number\n  subfeatures: MinimalFeature[]\n}\n\nexport function ucscProcessedTranscript(feature: TranscriptFeat) {\n  const {\n    subfeatures: oldSubfeatures,\n    thickStart,\n    thickEnd,\n    blockCount,\n    blockSizes,\n    chromStarts,\n    refName,\n    strand = 0,\n    ...rest\n  } = feature\n\n  if (!thickStart || !thickEnd || !strand) {\n    return feature\n  }\n\n  const subfeatures: MinimalFeature[] = []\n  oldSubfeatures\n    .filter(child => child.type === 'block')\n    .sort((a, b) => a.start - b.start)\n    .forEach(block => {\n      const start = block.start\n      const end = block.end\n      if (thickStart >= end) {\n        // left-side UTR\n        const prime = strand > 0 ? 'five' : 'three'\n        subfeatures.push({\n          type: `${prime}_prime_UTR`,\n          start,\n          end,\n          refName,\n        })\n      } else if (thickStart > start && thickStart < end && thickEnd >= end) {\n        // UTR | CDS\n        const prime = strand > 0 ? 'five' : 'three'\n        subfeatures.push(\n          {\n            type: `${prime}_prime_UTR`,\n            start,\n            end: thickStart,\n            refName,\n          },\n          {\n            type: 'CDS',\n            start: thickStart,\n            end,\n            refName,\n          },\n        )\n      } else if (thickStart <= start && thickEnd >= end) {\n        // CDS\n        subfeatures.push({\n          type: 'CDS',\n          start,\n          end,\n          refName,\n        })\n      } else if (thickStart > start && thickStart < end && thickEnd < end) {\n        // UTR | CDS | UTR\n        const leftPrime = strand > 0 ? 'five' : 'three'\n        const rightPrime = strand > 0 ? 'three' : 'five'\n        subfeatures.push(\n          {\n            type: `${leftPrime}_prime_UTR`,\n            start,\n            end: thickStart,\n            refName,\n          },\n          {\n            type: 'CDS',\n            start: thickStart,\n            end: thickEnd,\n            refName,\n          },\n          {\n            type: `${rightPrime}_prime_UTR`,\n            start: thickEnd,\n            end,\n            refName,\n          },\n        )\n      } else if (thickStart <= start && thickEnd > start && thickEnd < end) {\n        // CDS | UTR\n        const prime = strand > 0 ? 'three' : 'five'\n        subfeatures.push(\n          {\n            type: 'CDS',\n            start,\n            end: thickEnd,\n            refName,\n          },\n          {\n            type: `${prime}_prime_UTR`,\n            start: thickEnd,\n            end,\n            refName,\n          },\n        )\n      } else if (thickEnd <= start) {\n        // right-side UTR\n        const prime = strand > 0 ? 'three' : 'five'\n        subfeatures.push({\n          type: `${prime}_prime_UTR`,\n          start,\n          end,\n          refName,\n        })\n      }\n    })\n\n  return { ...rest, strand, type: 'mRNA', refName, subfeatures }\n}\n\nfunction defaultParser(fields: string[], line: string) {\n  const obj = Object.fromEntries(\n    line.split('\\t').map((f, i) => [fields[i]!, f] as const),\n  )\n  const {\n    blockStarts,\n    blockCount,\n    chromStarts,\n    thickEnd,\n    thickStart,\n    blockSizes,\n    ...rest\n  } = obj\n\n  return {\n    ...rest,\n    blockStarts: blockStarts?.split(',').map(r => +r),\n    chromStarts: chromStarts?.split(',').map(r => +r),\n    blockSizes: blockSizes?.split(',').map(r => +r),\n    thickStart: thickStart ? +thickStart : undefined,\n    thickEnd: thickEnd ? +thickEnd : undefined,\n    blockCount: blockCount ? +blockCount : undefined,\n  } as Record<string, unknown>\n}\n\nexport function makeBlocks({\n  start,\n  uniqueId,\n  refName,\n  chromStarts,\n  blockCount,\n  blockSizes,\n  blockStarts,\n}: {\n  blockCount: number\n  start: number\n  uniqueId: string\n  refName: string\n  chromStarts?: number[]\n  blockSizes: number[]\n  blockStarts?: number[]\n}) {\n  const subfeatures = []\n  const starts = chromStarts || blockStarts || []\n  for (let b = 0; b < blockCount; b++) {\n    const bmin = (starts[b] || 0) + start\n    const bmax = bmin + (blockSizes[b] || 0)\n    subfeatures.push({\n      uniqueId: `${uniqueId}-${b}`,\n      start: bmin,\n      end: bmax,\n      refName,\n      type: 'block',\n    })\n  }\n  return subfeatures\n}\nexport function featureData(\n  line: string,\n  colRef: number,\n  colStart: number,\n  colEnd: number,\n  scoreColumn: string,\n  parser: BED,\n  uniqueId: string,\n  names?: string[],\n) {\n  const l = line.split('\\t')\n  const refName = l[colRef]!\n  const start = +l[colStart]!\n  const colSame = colStart === colEnd ? 1 : 0\n  const end = +l[colEnd]! + colSame\n  const data = names\n    ? defaultParser(names, line)\n    : parser.parseLine(line, { uniqueId })\n\n  const {\n    blockCount,\n    blockSizes,\n    blockStarts,\n    chromStarts,\n    thickStart,\n    thickEnd,\n    type,\n    score,\n    chrom: _1,\n    chromStart: _2,\n    chromEnd: _3,\n    ...rest\n  } = data\n  const subfeatures = blockCount\n    ? makeBlocks({\n        start,\n        uniqueId,\n        refName,\n        chromStarts,\n        blockCount,\n        blockSizes,\n        blockStarts,\n      })\n    : []\n  const f = {\n    ...rest,\n    type,\n    score: scoreColumn ? +data[scoreColumn] : score,\n    start,\n    end,\n    refName,\n    uniqueId,\n    subfeatures,\n  }\n  return new SimpleFeature({\n    id: uniqueId,\n    data: isUcscProcessedTranscript(data)\n      ? ucscProcessedTranscript({\n          thickStart: thickStart!,\n          thickEnd: thickEnd!,\n          blockCount: blockCount!,\n          blockSizes: blockSizes!,\n          chromStarts: chromStarts,\n          ...f,\n        })\n      : f,\n  })\n}\n\nexport function isUcscProcessedTranscript(f: {\n  thickStart?: number\n  blockCount?: number\n  strand?: number\n}) {\n  return f.thickStart && f.blockCount && f.strand !== 0\n}\n"],"names":["BedAdapter","BaseFeatureDataAdapter","intervalTrees","loadDataP","opts","pm","this","pluginManager","bedLoc","getConf","buf","openLocation","readFile","buffer","isGzip","unzip","length","Error","lines","TextDecoder","fatal","decode","split","filter","f","headerLines","i","startsWith","push","header","join","features","line","tab","indexOf","refName","slice","autoSql","parser","BED","columnNames","scoreColumn","colRef","colStart","colEnd","loadData","bedFeatures","catch","e","undefined","getRefNames","Object","keys","getHeader","getNames","defline","at","includes","map","field","trim","loadFeatureIntervalTreeHelper","names","intervalTree","IntervalTree","ret","uniqueId","id","featureData","obj","insert","get","loadFeatureIntervalTree","getFeatures","query","ObservableCreate","async","start","end","search","forEach","observer","next","complete","signal","freeResources","ucscProcessedTranscript","feature","subfeatures","oldSubfeatures","thickStart","thickEnd","blockCount","blockSizes","chromStarts","strand","rest","child","type","sort","a","b","block","prime","leftPrime","rightPrime","makeBlocks","blockStarts","starts","bmin","bmax","l","colSame","data","fields","fromEntries","r","defaultParser","parseLine","score","chrom","_1","chromStart","_2","chromEnd","_3","SimpleFeature","isUcscProcessedTranscript"],"sourceRoot":""}
\ No newline at end of file