view x/static/js/9280.6e897b98.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

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BigInt32 = BigInt(32)\n\nexport function getBigInt64(\n  dataView: DataView,\n  byteOffset: number,\n  littleEndian: boolean | undefined,\n): bigint {\n  const littleEndianMask = Number(!!littleEndian)\n  const bigEndianMask = Number(!littleEndian)\n\n  return (\n    (BigInt(\n      dataView.getInt32(byteOffset, littleEndian) * bigEndianMask +\n        dataView.getInt32(byteOffset + 4, littleEndian) * littleEndianMask,\n    ) <<\n      BigInt32) |\n    BigInt(\n      dataView.getUint32(byteOffset, littleEndian) * littleEndianMask +\n        dataView.getUint32(byteOffset + 4, littleEndian) * bigEndianMask,\n    )\n  )\n}\n\nexport function getBigUint64(\n  dataView: DataView,\n  byteOffset: number,\n  littleEndian: boolean | undefined,\n): bigint {\n  const a = dataView.getUint32(byteOffset, littleEndian)\n  const b = dataView.getUint32(byteOffset + 4, littleEndian)\n\n  const littleEndianMask = Number(!!littleEndian)\n  const bigEndianMask = Number(!littleEndian)\n\n  // This branch-less optimization is 77x faster than normal ternary operator.\n  // and only 3% slower than native implementation\n  // https://jsbench.me/p8kyhg1eqv/1\n  return (\n    (BigInt(a * bigEndianMask + b * littleEndianMask) << BigInt32) |\n    BigInt(a * littleEndianMask + b * bigEndianMask)\n  )\n}\n","import { getBigInt64, getBigUint64 } from './pure'\n\nif (!('getBigInt64' in DataView)) {\n  DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {\n    return getBigInt64(this, byteOffset, littleEndian)\n  }\n}\n\nif (!('getBigUint64' in DataView)) {\n  DataView.prototype.getBigUint64 = function (byteOffset, littleEndian) {\n    return getBigUint64(this, byteOffset, littleEndian)\n  }\n}\n","import { LocalFile, GenericFilehandle } from 'generic-filehandle'\nimport { Buffer } from 'buffer'\n\nconst TWOBIT_MAGIC = 0x1a412743\n\nfunction tinyMemoize(_class: any, methodName: string) {\n  const method = _class.prototype[methodName]\n  const memoAttributeName = `_memo_${methodName}`\n  _class.prototype[methodName] = function _tinyMemoized() {\n    if (!(memoAttributeName in this)) {\n      this[memoAttributeName] = method.call(this)\n    }\n    return this[memoAttributeName]\n  }\n}\n\nconst twoBit = ['T', 'C', 'A', 'G']\n// byteTo4Bases is an array of byteValue -> 'ACTG'\nconst byteTo4Bases = [] as string[]\nfor (let index = 0; index < 256; index++) {\n  byteTo4Bases.push(\n    twoBit[(index >> 6) & 3] +\n      twoBit[(index >> 4) & 3] +\n      twoBit[(index >> 2) & 3] +\n      twoBit[index & 3],\n  )\n}\n\nconst maskedByteTo4Bases = byteTo4Bases.map(bases => bases.toLowerCase())\n\nexport default class TwoBitFile {\n  private filehandle: GenericFilehandle\n  private version?: number\n\n  /**\n   * @param {object} args\n   * @param {string} [args.path] filesystem path for the .2bit file to open\n   * @param {Filehandle} [args.filehandle] node fs.promises-like filehandle for the .2bit file.\n   *  Only needs to support `filehandle.read(buffer, offset, length, position)`\n   */\n  constructor({\n    filehandle,\n    path,\n  }: {\n    filehandle?: GenericFilehandle\n    path?: string\n  }) {\n    if (filehandle) {\n      this.filehandle = filehandle\n    } else if (path) {\n      this.filehandle = new LocalFile(path)\n    } else {\n      throw new Error('must supply path or filehandle')\n    }\n  }\n\n  async _detectEndianness() {\n    const returnValue = await this.filehandle.read(\n      Buffer.allocUnsafe(8),\n      0,\n      8,\n      0,\n    )\n    const { buffer } = returnValue\n    if (buffer.readInt32LE(0) === TWOBIT_MAGIC) {\n      this.version = buffer.readInt32LE(4)\n    } else if (buffer.readInt32BE(0) === TWOBIT_MAGIC) {\n      throw new Error('big endian not supported')\n    } else {\n      throw new Error('not a 2bit file')\n    }\n  }\n\n  // memoize\n  /**\n   * @returns {Promise} for object with the file's header information, like\n   *  `{ magic: 0x1a412743, version: 0, sequenceCount: 42, reserved: 0 }`\n   */\n  async getHeader() {\n    await this._detectEndianness()\n\n    const { buffer } = await this.filehandle.read(\n      Buffer.allocUnsafe(16),\n      0,\n      16,\n      0,\n    )\n\n    const b = buffer\n    const le = true\n    const dataView = new DataView(b.buffer, b.byteOffset, b.length)\n    let offset = 0\n    const magic = dataView.getInt32(offset, le)\n    offset += 4\n    if (magic !== 0x1a412743) {\n      throw new Error(`Wrong magic number ${magic}`)\n    }\n    const version = dataView.getInt32(offset, le)\n    offset += 4\n    const sequenceCount = dataView.getUint32(offset, le)\n    offset += 4\n    const reserved = dataView.getUint32(offset, le)\n\n    return { version, magic, sequenceCount, reserved }\n  }\n\n  // memoize\n  /**\n   * @returns {Promise} for object with the file's index of offsets, like `{ seqName: fileOffset, ...}`\n   */\n  async getIndex() {\n    const header = await this.getHeader()\n    const maxIndexLength =\n      8 + header.sequenceCount * (1 + 256 + (this.version === 1 ? 8 : 4))\n    const { buffer } = await this.filehandle.read(\n      Buffer.allocUnsafe(maxIndexLength),\n      0,\n      maxIndexLength,\n      8,\n    )\n\n    const le = true\n    const b = buffer\n    const dataView = new DataView(b.buffer, b.byteOffset, b.length)\n    let offset = 0\n    const sequenceCount = dataView.getUint32(offset, le)\n    offset += 4\n    // const reserved = dataView.getUint32(offset, le)\n    offset += 4\n    const indexData = []\n    for (let i = 0; i < sequenceCount; i++) {\n      const nameLength = dataView.getUint8(offset)\n      offset += 1\n      const name = buffer.subarray(offset, offset + nameLength).toString()\n      offset += nameLength\n      if (header.version === 1) {\n        const dataOffset = Number(dataView.getBigUint64(offset, le))\n        offset += 8\n        indexData.push({ offset: dataOffset, name })\n      } else {\n        const dataOffset = dataView.getUint32(offset, le)\n        offset += 4\n        indexData.push({ offset: dataOffset, name })\n      }\n    }\n\n    return Object.fromEntries(\n      indexData.map(({ name, offset }) => [name, offset]),\n    )\n  }\n\n  /**\n   * @returns {Promise} for an array of string sequence names that are found in the file\n   */\n  async getSequenceNames() {\n    const index = await this.getIndex()\n    return Object.keys(index)\n  }\n\n  /**\n   * @returns {Promise} for an object listing the lengths of all sequences like\n   * `{seqName: length, ...}`.\n   *\n   * note: this is a relatively slow operation especially if there are many\n   * refseqs in the file, if you can get this information from a different file\n   * e.g. a chrom.sizes file, it will be much faster\n   */\n  async getSequenceSizes() {\n    const index = await this.getIndex()\n    const seqNames = Object.keys(index)\n    const sizePromises = Object.values(index).map(offset =>\n      this._getSequenceSize(offset),\n    )\n    const sizes = await Promise.all(sizePromises)\n    const returnObject = {} as Record<string, number>\n    for (const [index_, seqName] of seqNames.entries()) {\n      returnObject[seqName] = sizes[index_]\n    }\n    return returnObject\n  }\n\n  /**\n   * @param {string} seqName name of the sequence\n   * @returns {Promise} for the sequence's length, or undefined if it is not in the file\n   */\n  async getSequenceSize(seqName: string) {\n    const index = await this.getIndex()\n    const offset = index[seqName]\n    if (!offset) {\n      return undefined\n    }\n    return this._getSequenceSize(offset)\n  }\n\n  async _getSequenceSize(offset: number) {\n    return this._record1(offset).then(f => f.dnaSize)\n  }\n\n  async _record1(offset2: number, len = 8) {\n    const { buffer } = await this.filehandle.read(\n      Buffer.allocUnsafe(len),\n      0,\n      len,\n      offset2,\n    )\n    const b = buffer\n    const le = true\n    let offset = 0\n    const dataView = new DataView(b.buffer, b.byteOffset, b.length)\n\n    const dnaSize = dataView.getUint32(offset, le)\n    offset += 4\n    const nBlockCount = dataView.getUint32(offset, le)\n    offset += 4\n    return { dnaSize, nBlockCount }\n  }\n\n  async _record2(offset2: number, len: number) {\n    const { buffer } = await this.filehandle.read(\n      Buffer.allocUnsafe(len),\n      0,\n      len,\n      offset2,\n    )\n    const b = buffer\n    const le = true\n    let offset = 0\n    const dataView = new DataView(b.buffer, b.byteOffset, b.length)\n\n    const nBlockCount = dataView.getUint32(offset, le)\n    offset += 4\n    const nBlockStarts = [] as number[]\n    for (let i = 0; i < nBlockCount; i++) {\n      const elt = dataView.getUint32(offset, le)\n      offset += 4\n      nBlockStarts.push(elt)\n    }\n    const nBlockSizes = [] as number[]\n    for (let i = 0; i < nBlockCount; i++) {\n      const elt = dataView.getUint32(offset, le)\n      offset += 4\n      nBlockSizes.push(elt)\n    }\n    const maskBlockCount = dataView.getUint32(offset, le)\n    return {\n      maskBlockCount,\n      nBlockSizes,\n      nBlockStarts,\n    }\n  }\n  async _record3(offset2: number, len: number) {\n    const { buffer } = await this.filehandle.read(\n      Buffer.allocUnsafe(len),\n      0,\n      len,\n      offset2,\n    )\n    const b = buffer\n    const le = true\n    let offset = 0\n    const dataView = new DataView(b.buffer, b.byteOffset, b.length)\n\n    const maskBlockCount = dataView.getUint32(offset, le)\n    offset += 4\n    const maskBlockStarts = [] as number[]\n    for (let i = 0; i < maskBlockCount; i++) {\n      const elt = dataView.getUint32(offset, le)\n      offset += 4\n      maskBlockStarts.push(elt)\n    }\n    const maskBlockSizes = [] as number[]\n    for (let i = 0; i < maskBlockCount; i++) {\n      const elt = dataView.getUint32(offset, le)\n      offset += 4\n      maskBlockSizes.push(elt)\n    }\n    const reserved = dataView.getInt32(offset, le)\n    return {\n      maskBlockCount,\n      maskBlockSizes,\n      maskBlockStarts,\n      reserved,\n    }\n  }\n\n  async _getSequenceRecord(offset: number) {\n    const rec1 = await this._record1(offset)\n    const rec2DataLen = rec1.nBlockCount * 8 + 8\n    const rec2 = await this._record2(offset + 4, rec2DataLen)\n    const rec3DataLen = rec2.maskBlockCount * 8 + 8\n    const rec3 = await this._record3(offset + 4 + rec2DataLen - 4, rec3DataLen)\n\n    const rec = {\n      dnaSize: rec1.dnaSize,\n      nBlocks: {\n        starts: rec2.nBlockStarts,\n        sizes: rec2.nBlockSizes,\n      },\n      maskBlocks: {\n        starts: rec3.maskBlockStarts,\n        sizes: rec3.maskBlockSizes,\n      },\n      dnaPosition: offset + 4 + rec2DataLen - 4 + rec3DataLen,\n    }\n    return rec\n  }\n\n  /**\n   * @param {string} seqName name of the sequence you want\n   * @param {number} [regionStart] optional 0-based half-open start of the sequence region to fetch.\n   * @param {number} [regionEnd] optional 0-based half-open end of the sequence region to fetch. defaults to end of the sequence\n   * @returns {Promise} for a string of sequence bases\n   */\n  async getSequence(\n    seqName: string,\n    regionStart = 0,\n    regionEnd = Number.POSITIVE_INFINITY,\n  ) {\n    const index = await this.getIndex()\n    const offset = index[seqName]\n    if (!offset) {\n      return undefined\n    }\n    // fetch the record for the seq\n    const record = await this._getSequenceRecord(offset)\n\n    if (regionStart < 0) {\n      throw new TypeError('regionStart cannot be less than 0')\n    }\n    // end defaults to the end of the sequence\n    if (regionEnd === undefined || regionEnd > record.dnaSize) {\n      regionEnd = record.dnaSize\n    }\n\n    const nBlocks = this._getOverlappingBlocks(\n      regionStart,\n      regionEnd,\n      record.nBlocks.starts,\n      record.nBlocks.sizes,\n    )\n    const maskBlocks = this._getOverlappingBlocks(\n      regionStart,\n      regionEnd,\n      record.maskBlocks.starts,\n      record.maskBlocks.sizes,\n    )\n\n    const baseBytes = Buffer.allocUnsafe(\n      Math.ceil((regionEnd - regionStart) / 4) + 1,\n    )\n    const baseBytesOffset = Math.floor(regionStart / 4)\n    const { buffer } = await this.filehandle.read(\n      baseBytes,\n      0,\n      baseBytes.length,\n      record.dnaPosition + baseBytesOffset,\n    )\n\n    let sequenceBases = ''\n    for (\n      let genomicPosition = regionStart;\n      genomicPosition < regionEnd;\n      genomicPosition += 1\n    ) {\n      // check whether we are currently masked\n      while (maskBlocks.length > 0 && maskBlocks[0].end <= genomicPosition) {\n        maskBlocks.shift()\n      }\n      const baseIsMasked =\n        maskBlocks[0] &&\n        maskBlocks[0].start <= genomicPosition &&\n        maskBlocks[0].end > genomicPosition\n\n      // process the N block if we have one\n      if (\n        nBlocks[0] &&\n        genomicPosition >= nBlocks[0].start &&\n        genomicPosition < nBlocks[0].end\n      ) {\n        const currentNBlock = nBlocks.shift()\n        for (\n          ;\n          genomicPosition < currentNBlock.end && genomicPosition < regionEnd;\n          genomicPosition += 1\n        ) {\n          sequenceBases += baseIsMasked ? 'n' : 'N'\n        }\n        genomicPosition -= 1\n      } else {\n        const bytePosition = Math.floor(genomicPosition / 4) - baseBytesOffset\n        const subPosition = genomicPosition % 4\n        const byte = buffer[bytePosition]\n        sequenceBases += baseIsMasked\n          ? maskedByteTo4Bases[byte][subPosition]\n          : byteTo4Bases[byte][subPosition]\n      }\n    }\n\n    return sequenceBases\n  }\n\n  _getOverlappingBlocks(\n    regionStart: number,\n    regionEnd: number,\n    blockStarts: number[],\n    blockSizes: number[],\n  ) {\n    // find the start and end indexes of the blocks that match\n    let startIndex: number | undefined\n    let endIndex: number | undefined\n    for (const [index, blockStart] of blockStarts.entries()) {\n      const blockSize = blockSizes[index]\n      if (regionStart >= blockStart + blockSize || regionEnd <= blockStart) {\n        // block does not overlap the region\n        if (startIndex !== undefined) {\n          endIndex = index\n          break\n        }\n      } else if (startIndex === undefined) {\n        startIndex = index\n      } // block does overlap the region, record this if it is the first\n    }\n\n    if (startIndex === undefined) {\n      return []\n    }\n\n    // now format some block objects to return\n    if (endIndex === undefined) {\n      endIndex = blockStarts.length\n    }\n\n    const blocks = new Array(endIndex - startIndex)\n    for (\n      let blockNumber = startIndex;\n      blockNumber < endIndex;\n      blockNumber += 1\n    ) {\n      blocks[blockNumber - startIndex] = {\n        start: blockStarts[blockNumber],\n        end: blockStarts[blockNumber] + blockSizes[blockNumber],\n        size: blockSizes[blockNumber],\n      }\n    }\n    return blocks\n  }\n}\n\ntinyMemoize(TwoBitFile, 'getIndex')\ntinyMemoize(TwoBitFile, 'getHeader')\n","import { BaseSequenceAdapter } 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 SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { TwoBitFile } from '@gmod/twobit'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\nexport default class TwoBitAdapter extends BaseSequenceAdapter {\n  private twobit: TwoBitFile\n\n  // the chromSizesData can be used to speed up loading since TwoBit has to do\n  // many range requests at startup to perform the getRegions request\n  protected chromSizesData: Promise<Record<string, number> | undefined>\n\n  private async initChromSizes() {\n    const conf = readConfObject(this.config, 'chromSizesLocation')\n    // check against default and empty in case someone makes the field blank in\n    // config editor, may want better way to check \"optional config slots\" in\n    // future\n    if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {\n      const file = openLocation(conf, this.pluginManager)\n      const data = await file.readFile('utf8')\n      return Object.fromEntries(\n        data\n          .split(/\\n|\\r\\n|\\r/)\n          .filter(line => !!line.trim())\n          .map(line => {\n            const [name, length] = line.split('\\t')\n            return [name!, +length!]\n          }),\n      )\n    }\n    return undefined\n  }\n\n  constructor(\n    config: AnyConfigurationModel,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const pm = this.pluginManager\n    this.chromSizesData = this.initChromSizes()\n    this.twobit = new TwoBitFile({\n      filehandle: openLocation(this.getConf('twoBitLocation'), pm),\n    })\n  }\n\n  public async getRefNames() {\n    const chromSizesData = await this.chromSizesData\n    if (chromSizesData) {\n      return Object.keys(chromSizesData)\n    }\n    return this.twobit.getSequenceNames()\n  }\n\n  public async getRegions(): Promise<NoAssemblyRegion[]> {\n    const chromSizesData = await this.chromSizesData\n    if (chromSizesData) {\n      return Object.keys(chromSizesData).map(refName => ({\n        refName,\n        start: 0,\n        end: chromSizesData[refName]!,\n      }))\n    }\n    const refSizes = await this.twobit.getSequenceSizes()\n    return Object.keys(refSizes).map(refName => ({\n      refName,\n      start: 0,\n      end: refSizes[refName]!,\n    }))\n  }\n\n  /**\n   * Fetch features for a certain region\n   * @param param -\n   * @returns Observable of Feature objects in the region\n   */\n  public getFeatures({ refName, start, end }: NoAssemblyRegion) {\n    return ObservableCreate<Feature>(async observer => {\n      const size = await this.twobit.getSequenceSize(refName)\n      const regionEnd = size !== undefined ? Math.min(size, end) : end\n      const seq = await this.twobit.getSequence(refName, start, regionEnd)\n      if (seq) {\n        observer.next(\n          new SimpleFeature({\n            id: `${refName} ${start}-${regionEnd}`,\n            data: { refName, start, end: regionEnd, seq },\n          }),\n        )\n      }\n      observer.complete()\n    })\n  }\n\n  /**\n   * called to provide a hint that data tied to a certain region\n   * will not be needed for the foreseeable future and can be purged\n   * from caches, etc\n   */\n  public freeResources(/* { region } */): void {}\n}\n"],"names":["BigInt32","BigInt","DataView","prototype","getBigInt64","byteOffset","littleEndian","dataView","littleEndianMask","Number","bigEndianMask","getInt32","getUint32","this","getBigUint64","a","b","TWOBIT_MAGIC","tinyMemoize","_class","methodName","method","memoAttributeName","call","twoBit","byteTo4Bases","index","push","maskedByteTo4Bases","map","bases","toLowerCase","TwoBitFile","constructor","filehandle","path","Error","_detectEndianness","returnValue","read","allocUnsafe","buffer","readInt32LE","readInt32BE","version","getHeader","le","length","offset","magic","sequenceCount","reserved","getIndex","header","maxIndexLength","indexData","i","nameLength","getUint8","name","subarray","toString","dataOffset","Object","fromEntries","getSequenceNames","keys","getSequenceSizes","seqNames","sizePromises","values","_getSequenceSize","sizes","Promise","all","returnObject","index_","seqName","entries","getSequenceSize","_record1","then","f","dnaSize","offset2","len","nBlockCount","_record2","nBlockStarts","elt","nBlockSizes","maskBlockCount","_record3","maskBlockStarts","maskBlockSizes","_getSequenceRecord","rec1","rec2DataLen","rec2","rec3DataLen","rec3","nBlocks","starts","maskBlocks","dnaPosition","getSequence","regionStart","regionEnd","POSITIVE_INFINITY","record","TypeError","undefined","_getOverlappingBlocks","baseBytes","Math","ceil","baseBytesOffset","floor","sequenceBases","genomicPosition","end","shift","baseIsMasked","start","currentNBlock","subPosition","byte","blockStarts","blockSizes","startIndex","endIndex","blockStart","blocks","Array","blockNumber","size","TwoBitAdapter","BaseSequenceAdapter","initChromSizes","conf","readConfObject","config","uri","file","openLocation","pluginManager","data","readFile","split","filter","line","trim","getSubAdapter","super","pm","chromSizesData","twobit","getConf","getRefNames","getRegions","refName","refSizes","getFeatures","ObservableCreate","async","min","seq","observer","next","SimpleFeature","id","complete","freeResources"],"sourceRoot":""}