comparison x/static/js/4284.61dbc58f.chunk.js.map @ 125:49f3d3878413 draft

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

125:49f3d3878413

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{ unzip } from '@gmod/bgzf-filehandle'\n\n// locals\nimport { isGzip, SimpleFeature } from '../../util'\nimport { openLocation } from '../../util/io'\nimport { BaseAdapter } from '../BaseAdapter'\n\nexport default class CytobandAdapter extends BaseAdapter {\n  async getData() {\n    const pm = this.pluginManager\n    const loc = this.getConf('cytobandLocation')\n    if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {\n      return []\n    }\n    const buffer = await openLocation(loc, pm).readFile()\n    const buf = isGzip(buffer) ? await unzip(buffer) : buffer\n    const text = new TextDecoder('utf8', { fatal: true }).decode(buf)\n    return text\n      .split(/\\n|\\r\\n|\\r/)\n      .filter(f => !!f.trim())\n      .map((line, i) => {\n        const [refName, start, end, name, type] = line.split('\\t')\n        return new SimpleFeature({\n          uniqueId: `${i}`,\n          refName: refName!,\n          start: +start!,\n          end: +end!,\n          name: name!,\n          type: type!,\n        })\n      })\n  }\n\n  freeResources(/* { region } */): void {}\n}\n","import { Buffer } from 'buffer'\n//@ts-ignore\nimport { Z_SYNC_FLUSH, Inflate } from 'pako'\n\ninterface VirtualOffset {\n  blockPosition: number\n  dataPosition: number\n}\ninterface Chunk {\n  minv: VirtualOffset\n  maxv: VirtualOffset\n}\n\n// browserify-zlib, which is the zlib shim used by default in webpacked code,\n// does not properly uncompress bgzf chunks that contain more than\n// one bgzf block, so export an unzip function that uses pako directly\n// if we are running in a browser.\nasync function unzip(inputData: Buffer) {\n  try {\n    let strm\n    let pos = 0\n    let i = 0\n    const chunks = []\n    let totalSize = 0\n    let inflator\n    do {\n      const remainingInput = inputData.subarray(pos)\n      inflator = new Inflate()\n      //@ts-ignore\n      ;({ strm } = inflator)\n      inflator.push(remainingInput, Z_SYNC_FLUSH)\n      if (inflator.err) {\n        throw new Error(inflator.msg)\n      }\n\n      pos += strm.next_in\n      chunks[i] = inflator.result as Uint8Array\n      totalSize += chunks[i].length\n      i += 1\n    } while (strm.avail_in)\n\n    const result = new Uint8Array(totalSize)\n    for (let i = 0, offset = 0; i < chunks.length; i++) {\n      result.set(chunks[i], offset)\n      offset += chunks[i].length\n    }\n    return Buffer.from(result)\n  } catch (e) {\n    //cleanup error message\n    if (`${e}`.match(/incorrect header check/)) {\n      throw new Error(\n        'problem decompressing block: incorrect gzip header check',\n      )\n    }\n    throw e\n  }\n}\n\n// similar to pakounzip, except it does extra counting\n// to return the positions of compressed and decompressed\n// data offsets\nasync function unzipChunk(inputData: Buffer) {\n  try {\n    let strm\n    let cpos = 0\n    let dpos = 0\n    const blocks = []\n    const cpositions = []\n    const dpositions = []\n    do {\n      const remainingInput = inputData.slice(cpos)\n      const inflator = new Inflate()\n      // @ts-ignore\n      ;({ strm } = inflator)\n      inflator.push(remainingInput, Z_SYNC_FLUSH)\n      if (inflator.err) {\n        throw new Error(inflator.msg)\n      }\n\n      const buffer = Buffer.from(inflator.result)\n      blocks.push(buffer)\n\n      cpositions.push(cpos)\n      dpositions.push(dpos)\n\n      cpos += strm.next_in\n      dpos += buffer.length\n    } while (strm.avail_in)\n\n    const buffer = Buffer.concat(blocks)\n    return { buffer, cpositions, dpositions }\n  } catch (e) {\n    //cleanup error message\n    if (`${e}`.match(/incorrect header check/)) {\n      throw new Error(\n        'problem decompressing block: incorrect gzip header check',\n      )\n    }\n    throw e\n  }\n}\n\n// similar to unzipChunk above but slices (0,minv.dataPosition) and\n// (maxv.dataPosition,end) off\nasync function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {\n  try {\n    let strm\n    const { minv, maxv } = chunk\n    let cpos = minv.blockPosition\n    let dpos = minv.dataPosition\n    const chunks = []\n    const cpositions = []\n    const dpositions = []\n\n    let totalSize = 0\n    let i = 0\n    do {\n      const remainingInput = inputData.subarray(cpos - minv.blockPosition)\n      const inflator = new Inflate()\n      // @ts-ignore\n      ;({ strm } = inflator)\n      inflator.push(remainingInput, Z_SYNC_FLUSH)\n      if (inflator.err) {\n        throw new Error(inflator.msg)\n      }\n\n      const buffer = inflator.result\n      chunks.push(buffer as Uint8Array)\n      let len = buffer.length\n\n      cpositions.push(cpos)\n      dpositions.push(dpos)\n      if (chunks.length === 1 && minv.dataPosition) {\n        // this is the first chunk, trim it\n        chunks[0] = chunks[0].subarray(minv.dataPosition)\n        len = chunks[0].length\n      }\n      const origCpos = cpos\n      cpos += strm.next_in\n      dpos += len\n\n      if (origCpos >= maxv.blockPosition) {\n        // this is the last chunk, trim it and stop decompressing\n        // note if it is the same block is minv it subtracts that already\n        // trimmed part of the slice length\n\n        chunks[i] = chunks[i].subarray(\n          0,\n          maxv.blockPosition === minv.blockPosition\n            ? maxv.dataPosition - minv.dataPosition + 1\n            : maxv.dataPosition + 1,\n        )\n\n        cpositions.push(cpos)\n        dpositions.push(dpos)\n        totalSize += chunks[i].length\n        break\n      }\n      totalSize += chunks[i].length\n      i++\n    } while (strm.avail_in)\n\n    const result = new Uint8Array(totalSize)\n    for (let i = 0, offset = 0; i < chunks.length; i++) {\n      result.set(chunks[i], offset)\n      offset += chunks[i].length\n    }\n    const buffer = Buffer.from(result)\n\n    return { buffer, cpositions, dpositions }\n  } catch (e) {\n    //cleanup error message\n    if (`${e}`.match(/incorrect header check/)) {\n      throw new Error(\n        'problem decompressing block: incorrect gzip header check',\n      )\n    }\n    throw e\n  }\n}\n\nfunction nodeUnzip() {\n  throw new Error('nodeUnzip not implemented.')\n}\n\nexport { unzip, unzipChunk, unzipChunkSlice, unzip as pakoUnzip, nodeUnzip }\n","import Long from 'long'\nimport { Buffer } from 'buffer'\nimport { LocalFile, GenericFilehandle } from 'generic-filehandle'\n\n// const COMPRESSED_POSITION = 0\nconst UNCOMPRESSED_POSITION = 1\n\nexport default class GziIndex {\n  filehandle: GenericFilehandle\n\n  index?: any\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 TypeError('either filehandle or path must be defined')\n    }\n  }\n\n  _readLongWithOverflow(buf: Buffer, offset = 0, unsigned = true) {\n    //@ts-ignore\n    const long = Long.fromBytesLE(buf.slice(offset, offset + 8), unsigned)\n    if (\n      long.greaterThan(Number.MAX_SAFE_INTEGER) ||\n      long.lessThan(Number.MIN_SAFE_INTEGER)\n    ) {\n      throw new TypeError('integer overflow')\n    }\n\n    return long.toNumber()\n  }\n\n  _getIndex() {\n    if (!this.index) {\n      this.index = this._readIndex()\n    }\n    return this.index\n  }\n\n  async _readIndex() {\n    let buf = Buffer.allocUnsafe(8)\n    await this.filehandle.read(buf, 0, 8, 0)\n    const numEntries = this._readLongWithOverflow(buf, 0, true)\n    if (!numEntries) {\n      return [[0, 0]]\n    }\n\n    const entries = new Array(numEntries + 1)\n    entries[0] = [0, 0]\n\n    // TODO rewrite this to make an index-index that stays in memory\n    const bufSize = 8 * 2 * numEntries\n    if (bufSize > Number.MAX_SAFE_INTEGER) {\n      throw new TypeError('integer overflow')\n    }\n    buf = Buffer.allocUnsafe(bufSize)\n    await this.filehandle.read(buf, 0, bufSize, 8)\n    for (let entryNumber = 0; entryNumber < numEntries; entryNumber += 1) {\n      const compressedPosition = this._readLongWithOverflow(\n        buf,\n        entryNumber * 16,\n      )\n      const uncompressedPosition = this._readLongWithOverflow(\n        buf,\n        entryNumber * 16 + 8,\n      )\n      entries[entryNumber + 1] = [compressedPosition, uncompressedPosition]\n    }\n\n    return entries\n  }\n\n  async getLastBlock() {\n    const entries = await this._getIndex()\n    if (!entries.length) {\n      return undefined\n    }\n    return entries[entries.length - 1]\n  }\n\n  async getRelevantBlocksForRead(length: number, position: number) {\n    const endPosition = position + length\n    if (length === 0) {\n      return []\n    }\n    const entries = await this._getIndex()\n    const relevant = []\n\n    // binary search to find the block that the\n    // read starts in and extend forward from that\n    const compare = (entry: any, nextEntry: any) => {\n      const uncompressedPosition = entry[UNCOMPRESSED_POSITION]\n      const nextUncompressedPosition = nextEntry\n        ? nextEntry[UNCOMPRESSED_POSITION]\n        : Infinity\n      // block overlaps read start\n      if (\n        uncompressedPosition <= position &&\n        nextUncompressedPosition > position\n      ) {\n        return 0\n        // block is before read start\n      }\n      if (uncompressedPosition < position) {\n        return -1\n      }\n      // block is after read start\n      return 1\n    }\n\n    let lowerBound = 0\n    let upperBound = entries.length - 1\n    let searchPosition = Math.floor(entries.length / 2)\n\n    let comparison = compare(\n      entries[searchPosition],\n      entries[searchPosition + 1],\n    )\n    while (comparison !== 0) {\n      if (comparison > 0) {\n        upperBound = searchPosition - 1\n      } else if (comparison < 0) {\n        lowerBound = searchPosition + 1\n      }\n      searchPosition = Math.ceil((upperBound - lowerBound) / 2) + lowerBound\n      comparison = compare(entries[searchPosition], entries[searchPosition + 1])\n    }\n\n    // here's where we read forward\n    relevant.push(entries[searchPosition])\n    let i = searchPosition + 1\n    for (; i < entries.length; i += 1) {\n      relevant.push(entries[i])\n      if (entries[i][UNCOMPRESSED_POSITION] >= endPosition) {\n        break\n      }\n    }\n    if (relevant[relevant.length - 1][UNCOMPRESSED_POSITION] < endPosition) {\n      relevant.push([])\n    }\n    return relevant\n  }\n}\n","import { Buffer } from 'buffer'\nimport { LocalFile, GenericFilehandle } from 'generic-filehandle'\n\n// locals\nimport { unzip } from './unzip'\nimport GziIndex from './gziIndex'\n\nexport default class BgzFilehandle {\n  filehandle: GenericFilehandle\n  gzi: GziIndex\n\n  constructor({\n    filehandle,\n    path,\n    gziFilehandle,\n    gziPath,\n  }: {\n    filehandle?: GenericFilehandle\n    path?: string\n    gziFilehandle?: GenericFilehandle\n    gziPath?: string\n  }) {\n    if (filehandle) {\n      this.filehandle = filehandle\n    } else if (path) {\n      this.filehandle = new LocalFile(path)\n    } else {\n      throw new TypeError('either filehandle or path must be defined')\n    }\n\n    if (!gziFilehandle && !gziPath && !path) {\n      throw new TypeError('either gziFilehandle or gziPath must be defined')\n    }\n\n    this.gzi = new GziIndex({\n      filehandle: gziFilehandle,\n      path: !gziFilehandle && !gziPath && path ? gziPath : `${path}.gzi`,\n    })\n  }\n\n  async stat() {\n    const compressedStat = await this.filehandle.stat()\n    return Object.assign(compressedStat, {\n      size: await this.getUncompressedFileSize(),\n      blocks: undefined,\n      blksize: undefined,\n    })\n  }\n\n  async getUncompressedFileSize() {\n    // read the last block's ISIZE (see gzip RFC),\n    // and add it to its uncompressedPosition\n    const [, uncompressedPosition] = await this.gzi.getLastBlock()\n\n    const { size } = await this.filehandle.stat()\n\n    const buf = Buffer.allocUnsafe(4)\n    // note: there should be a 28-byte EOF marker (an empty block) at\n    // the end of the file, so we skip backward past that\n    const { bytesRead } = await this.filehandle.read(buf, 0, 4, size - 28 - 4)\n    if (bytesRead !== 4) {\n      throw new Error('read error')\n    }\n    const lastBlockUncompressedSize = buf.readUInt32LE(0)\n    return uncompressedPosition + lastBlockUncompressedSize\n  }\n\n  async _readAndUncompressBlock(\n    blockBuffer: Buffer,\n    [compressedPosition]: [number],\n    [nextCompressedPosition]: [number],\n  ) {\n    let next = nextCompressedPosition\n    if (!next) {\n      next = (await this.filehandle.stat()).size\n    }\n\n    // read the compressed data into the block buffer\n    const blockCompressedLength = next - compressedPosition\n\n    await this.filehandle.read(\n      blockBuffer,\n      0,\n      blockCompressedLength,\n      compressedPosition,\n    )\n\n    // uncompress it\n    const unzippedBuffer = await unzip(\n      blockBuffer.slice(0, blockCompressedLength),\n    )\n\n    return unzippedBuffer as Buffer\n  }\n\n  async read(buf: Buffer, offset: number, length: number, position: number) {\n    // get the block positions for this read\n    const blockPositions = await this.gzi.getRelevantBlocksForRead(\n      length,\n      position,\n    )\n    const blockBuffer = Buffer.allocUnsafe(32768 * 2)\n    // uncompress the blocks and read from them one at a time to keep memory usage down\n    let destinationOffset = offset\n    let bytesRead = 0\n    for (\n      let blockNum = 0;\n      blockNum < blockPositions.length - 1;\n      blockNum += 1\n    ) {\n      // eslint-disable-next-line no-await-in-loop\n      const uncompressedBuffer = await this._readAndUncompressBlock(\n        blockBuffer,\n        blockPositions[blockNum],\n        blockPositions[blockNum + 1],\n      )\n      const [, uncompressedPosition] = blockPositions[blockNum]\n      const sourceOffset =\n        uncompressedPosition >= position ? 0 : position - uncompressedPosition\n      const sourceEnd =\n        Math.min(\n          position + length,\n          uncompressedPosition + uncompressedBuffer.length,\n        ) - uncompressedPosition\n      if (sourceOffset >= 0 && sourceOffset < uncompressedBuffer.length) {\n        uncompressedBuffer.copy(buf, destinationOffset, sourceOffset, sourceEnd)\n        destinationOffset += sourceEnd - sourceOffset\n        bytesRead += sourceEnd - sourceOffset\n      }\n    }\n\n    return { bytesRead, buffer: buf }\n  }\n}\n"],"names":["CytobandAdapter","BaseAdapter","getData","pm","this","pluginManager","loc","getConf","uri","buffer","openLocation","readFile","buf","isGzip","unzip","TextDecoder","fatal","decode","split","filter","f","trim","map","line","i","refName","start","end","name","type","SimpleFeature","uniqueId","freeResources","async","inputData","strm","pos","chunks","inflator","totalSize","remainingInput","subarray","Inflate","push","Z_SYNC_FLUSH","err","Error","msg","next_in","result","length","avail_in","Uint8Array","offset","set","from","e","match","unzipChunkSlice","chunk","minv","maxv","cpos","blockPosition","dpos","dataPosition","cpositions","dpositions","len","origCpos","GziIndex","constructor","filehandle","path","TypeError","_readLongWithOverflow","unsigned","long","slice","greaterThan","Number","MAX_SAFE_INTEGER","lessThan","MIN_SAFE_INTEGER","toNumber","_getIndex","index","_readIndex","allocUnsafe","read","numEntries","entries","Array","bufSize","entryNumber","compressedPosition","uncompressedPosition","getLastBlock","getRelevantBlocksForRead","position","endPosition","relevant","compare","entry","nextEntry","nextUncompressedPosition","Infinity","lowerBound","upperBound","searchPosition","Math","floor","comparison","ceil","BgzFilehandle","gziFilehandle","gziPath","gzi","stat","compressedStat","Object","assign","size","getUncompressedFileSize","blocks","undefined","blksize","bytesRead","readUInt32LE","_readAndUncompressBlock","blockBuffer","nextCompressedPosition","next","blockCompressedLength","blockPositions","destinationOffset","blockNum","uncompressedBuffer","sourceOffset","sourceEnd","min","copy"],"sourceRoot":""}