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{ zip } from '../util'\n\nexport interface PAFRecord {\n  qname: string\n  qstart: number\n  qend: number\n  tname: string\n  tstart: number\n  tend: number\n  strand: number\n  extra: {\n    cg?: string\n    blockLen?: number\n    mappingQual: number\n    numMatches?: number\n    meanScore?: number\n  }\n}\n// based on \"weighted mean\" method from https://github.com/tpoorten/dotPlotly\n// License reproduced here\n//\n// MIT License\n\n// Copyright (c) 2017 Tom Poorten\n\n// Permission is hereby granted, free of charge, to any person obtaining a copy\n// of this software and associated documentation files (the \"Software\"), to deal\n// in the Software without restriction, including without limitation the rights\n// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n// copies of the Software, and to permit persons to whom the Software is\n// furnished to do so, subject to the following conditions:\n\n// The above copyright notice and this permission notice shall be included in all\n// copies or substantial portions of the Software.\n\n// THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n// SOFTWARE.\n//\n// Notes: in the weighted mean longer alignments factor in more heavily of all\n// the fragments of a query vs the reference that it mapped to\n//\n// this uses a combined key query+'-'+ref to iteratively map all the alignments\n// that match a particular ref from a particular query (so 1d array of what\n// could be a 2d map)\n//\n// the result is a single number that says e.g. chr5 from human mapped to chr5\n// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of\n// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more\n// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6.\n// this can show strong and weak levels of synteny, especially in polyploidy\n// situations\n\nexport function getWeightedMeans(ret: PAFRecord[]) {\n  const scoreMap: Record<string, { quals: number[]; len: number[] }> = {}\n  for (const entry of ret) {\n    const query = entry.qname\n    const target = entry.tname\n    const key = `${query}-${target}`\n    if (!scoreMap[key]) {\n      scoreMap[key] = { quals: [], len: [] }\n    }\n    scoreMap[key].quals.push(entry.extra.mappingQual)\n    scoreMap[key].len.push(entry.extra.blockLen || 1)\n  }\n\n  const meanScoreMap = Object.fromEntries(\n    Object.entries(scoreMap).map(([key, val]) => {\n      const vals = zip(val.quals, val.len)\n      return [key, weightedMean(vals)]\n    }),\n  )\n  for (const entry of ret) {\n    const query = entry.qname\n    const target = entry.tname\n    const key = `${query}-${target}`\n    entry.extra.meanScore = meanScoreMap[key]\n  }\n\n  let min = 10000\n  let max = 0\n  for (const entry of ret) {\n    min = Math.min(entry.extra.meanScore || 0, min)\n    max = Math.max(entry.extra.meanScore || 0, max)\n  }\n  for (const entry of ret) {\n    const b = entry.extra.meanScore || 0\n    entry.extra.meanScore = (b - min) / (max - min)\n  }\n\n  return ret\n}\n\n// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a\nfunction weightedMean(tuples: [number, number][]) {\n  const [valueSum, weightSum] = tuples.reduce(\n    ([valueSum, weightSum], [value, weight]) => [\n      valueSum + value * weight,\n      weightSum + weight,\n    ],\n    [0, 0],\n  )\n  return valueSum / weightSum\n}\n","import {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region } from '@jbrowse/core/util/types'\nimport { doesIntersect2 } from '@jbrowse/core/util/range'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature, isGzip } from '@jbrowse/core/util'\nimport {\n  AnyConfigurationModel,\n  readConfObject,\n} from '@jbrowse/core/configuration'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { MismatchParser } from '@jbrowse/plugin-alignments'\nimport type { Buffer } from 'buffer'\n\n// locals\nimport SyntenyFeature from '../SyntenyFeature'\nimport {\n  flipCigar,\n  swapIndelCigar,\n  parsePAFLine,\n  parseLineByLine,\n} from '../util'\nimport { getWeightedMeans, PAFRecord } from './util'\n\nconst { parseCigar } = MismatchParser\n\ninterface PAFOptions extends BaseOptions {\n  config?: AnyConfigurationModel\n}\n\nexport default class PAFAdapter extends BaseFeatureDataAdapter {\n  private setupP?: Promise<PAFRecord[]>\n\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  async setup(opts?: BaseOptions) {\n    if (!this.setupP) {\n      this.setupP = this.setupPre(opts).catch((e: unknown) => {\n        this.setupP = undefined\n        throw e\n      })\n    }\n    return this.setupP\n  }\n\n  async setupPre(opts?: BaseOptions) {\n    const pm = this.pluginManager\n    const pafLocation = openLocation(this.getConf('pafLocation'), pm)\n    const buffer = (await pafLocation.readFile(opts)) as Buffer\n    const buf = isGzip(buffer) ? await unzip(buffer) : buffer\n    return parseLineByLine(buf, parsePAFLine)\n  }\n\n  async hasDataForRefName() {\n    // determining this properly is basically a call to getFeatures\n    // so is not really that important, and has to be true or else\n    // getFeatures is never called (BaseAdapter filters it out)\n    return true\n  }\n\n  getAssemblyNames() {\n    const assemblyNames = this.getConf('assemblyNames') as string[]\n    if (assemblyNames.length === 0) {\n      const query = this.getConf('queryAssembly') as string\n      const target = this.getConf('targetAssembly') as string\n      return [query, target]\n    }\n    return assemblyNames\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    // @ts-expect-error\n    const r1 = opts.regions?.[0].assemblyName\n    const feats = await this.setup(opts)\n\n    const idx = this.getAssemblyNames().indexOf(r1)\n    if (idx !== -1) {\n      const set = new Set<string>()\n      for (const feat of feats) {\n        set.add(idx === 0 ? feat.qname : feat.tname)\n      }\n      return [...set]\n    }\n    console.warn('Unable to do ref renaming on adapter')\n    return []\n  }\n\n  getFeatures(query: Region, opts: PAFOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      let pafRecords = await this.setup(opts)\n      const { config } = opts\n\n      // note: this is not the adapter config, it is responding to a display\n      // setting passed in via the opts parameter\n      if (config && readConfObject(config, 'colorBy') === 'meanQueryIdentity') {\n        pafRecords = getWeightedMeans(pafRecords)\n      }\n      const assemblyNames = this.getAssemblyNames()\n\n      // The index of the assembly name in the query list corresponds to the\n      // adapter in the subadapters list\n      const { start: qstart, end: qend, refName: qref, assemblyName } = query\n      const index = assemblyNames.indexOf(assemblyName)\n\n      // if the getFeatures::query is on the query assembly, flip orientation\n      // of data\n      const flip = index === 0\n      if (index === -1) {\n        console.warn(`${assemblyName} not found in this adapter`)\n        observer.complete()\n      }\n\n      for (let i = 0; i < pafRecords.length; i++) {\n        const r = pafRecords[i]!\n        let start = 0\n        let end = 0\n        let refName = ''\n        let mateName = ''\n        let mateStart = 0\n        let mateEnd = 0\n\n        if (flip) {\n          start = r.qstart\n          end = r.qend\n          refName = r.qname\n          mateName = r.tname\n          mateStart = r.tstart\n          mateEnd = r.tend\n        } else {\n          start = r.tstart\n          end = r.tend\n          refName = r.tname\n          mateName = r.qname\n          mateStart = r.qstart\n          mateEnd = r.qend\n        }\n        const { extra, strand } = r\n        if (refName === qref && doesIntersect2(qstart, qend, start, end)) {\n          const { numMatches = 0, blockLen = 1, cg, ...rest } = extra\n\n          let CIGAR = extra.cg\n          if (extra.cg) {\n            if (flip && strand === -1) {\n              CIGAR = flipCigar(parseCigar(extra.cg)).join('')\n            } else if (flip) {\n              CIGAR = swapIndelCigar(extra.cg)\n            }\n          }\n\n          observer.next(\n            new SyntenyFeature({\n              uniqueId: i + assemblyName,\n              assemblyName,\n              start,\n              end,\n              type: 'match',\n              refName,\n              strand,\n              ...rest,\n              CIGAR,\n              syntenyId: i,\n              identity: numMatches / blockLen,\n              numMatches,\n              blockLen,\n              mate: {\n                start: mateStart,\n                end: mateEnd,\n                refName: mateName,\n                assemblyName: assemblyNames[+flip],\n              },\n            }),\n          )\n        }\n      }\n\n      observer.complete()\n    })\n  }\n\n  freeResources(/* { query } */): void {}\n}\n","import { SimpleFeature } from '@jbrowse/core/util'\nimport { MismatchParser } from '@jbrowse/plugin-alignments'\n\n// locals\nconst { getMismatches } = MismatchParser\n\nexport default class SyntenyFeature extends SimpleFeature {\n  get(arg: string): any {\n    if (arg === 'mismatches') {\n      return getMismatches(this.get('CIGAR'))\n    }\n    return super.get(arg)\n  }\n}\n","import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { isGzip } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n\nimport { PAFRecord } from './PAFAdapter/util'\n\nexport function parseBed(text: string) {\n  return new Map(\n    text\n      .split(/\\n|\\r\\n|\\r/)\n      .filter(f => !!f || f.startsWith('#'))\n      .map(line => {\n        const [refName, start, end, name, score, strand] = line.split('\\t')\n        return [\n          name,\n          {\n            refName,\n            start: +start!,\n            end: +end!,\n            score: +score!,\n            name,\n            strand: strand === '-' ? -1 : 1,\n          },\n        ]\n      }),\n  )\n}\n\nexport async function readFile(file: GenericFilehandle, opts?: BaseOptions) {\n  const buffer = (await file.readFile(opts)) as Buffer\n  return new TextDecoder('utf8', { fatal: true }).decode(\n    isGzip(buffer) ? await unzip(buffer) : buffer,\n  )\n}\n\nexport function zip(a: number[], b: number[]) {\n  return a.map((e, i) => [e, b[i]] as [number, number])\n}\n\nconst decoder =\n  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\nexport function parseLineByLine(\n  buffer: Buffer,\n  cb: (line: string) => PAFRecord,\n) {\n  let blockStart = 0\n  const entries = []\n  while (blockStart < buffer.length) {\n    const n = buffer.indexOf('\\n', blockStart)\n    if (n === -1) {\n      break\n    }\n    const b = buffer.subarray(blockStart, n)\n    const line = (decoder?.decode(b) || b.toString()).trim()\n    if (line) {\n      entries.push(cb(line))\n    }\n\n    blockStart = n + 1\n  }\n  return entries\n}\n\nexport function parsePAFLine(line: string) {\n  const [\n    qname,\n    ,\n    qstart,\n    qend,\n    strand,\n    tname,\n    ,\n    tstart,\n    tend,\n    numMatches,\n    blockLen,\n    mappingQual,\n    ...fields\n  ] = line.split('\\t')\n\n  const rest = Object.fromEntries(\n    fields.map(field => {\n      const r = field.indexOf(':')\n      const fieldName = field.slice(0, r)\n      const fieldValue = field.slice(r + 3)\n      return [fieldName, fieldValue]\n    }),\n  )\n\n  return {\n    tname,\n    tstart: +tstart!,\n    tend: +tend!,\n    qname,\n    qstart: +qstart!,\n    qend: +qend!,\n    strand: strand === '-' ? -1 : 1,\n    extra: {\n      numMatches: +numMatches!,\n      blockLen: +blockLen!,\n      mappingQual: +mappingQual!,\n      ...rest,\n    },\n  } as PAFRecord\n}\n\nexport function flipCigar(cigar: string[]) {\n  const arr = []\n  for (let i = cigar.length - 2; i >= 0; i -= 2) {\n    arr.push(cigar[i])\n    const op = cigar[i + 1]\n    if (op === 'D') {\n      arr.push('I')\n    } else if (op === 'I') {\n      arr.push('D')\n    } else {\n      arr.push(op)\n    }\n  }\n  return arr\n}\n\nexport function swapIndelCigar(cigar: string) {\n  return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I')\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":["weightedMean","tuples","valueSum","weightSum","reduce","value","weight","parseCigar","MismatchParser","PAFAdapter","BaseFeatureDataAdapter","setup","opts","this","setupP","setupPre","catch","e","undefined","pm","pluginManager","pafLocation","openLocation","getConf","buffer","readFile","buf","isGzip","unzip","parseLineByLine","parsePAFLine","hasDataForRefName","getAssemblyNames","assemblyNames","length","getRefNames","r1","regions","assemblyName","feats","idx","indexOf","set","Set","feat","add","qname","tname","console","warn","getFeatures","query","ObservableCreate","async","pafRecords","config","readConfObject","ret","scoreMap","entry","key","quals","len","push","extra","mappingQual","blockLen","meanScoreMap","Object","fromEntries","entries","map","val","zip","meanScore","min","max","Math","b","getWeightedMeans","start","qstart","end","qend","refName","qref","index","flip","observer","complete","i","r","mateName","mateStart","mateEnd","tstart","tend","strand","doesIntersect2","numMatches","cg","rest","CIGAR","flipCigar","join","swapIndelCigar","next","SyntenyFeature","uniqueId","type","syntenyId","identity","mate","freeResources","getMismatches","SimpleFeature","get","arg","super","parseBed","text","Map","split","filter","f","startsWith","line","name","score","file","TextDecoder","fatal","decode","a","decoder","cb","blockStart","n","subarray","toString","trim","fields","field","slice","cigar","arr","op","replaceAll","inputData","strm","pos","chunks","inflator","totalSize","remainingInput","Inflate","Z_SYNC_FLUSH","err","Error","msg","next_in","result","avail_in","Uint8Array","offset","from","match","unzipChunkSlice","chunk","minv","maxv","cpos","blockPosition","dpos","dataPosition","cpositions","dpositions","origCpos","GziIndex","constructor","filehandle","path","TypeError","_readLongWithOverflow","unsigned","long","greaterThan","Number","MAX_SAFE_INTEGER","lessThan","MIN_SAFE_INTEGER","toNumber","_getIndex","_readIndex","allocUnsafe","read","numEntries","Array","bufSize","entryNumber","compressedPosition","uncompressedPosition","getLastBlock","getRelevantBlocksForRead","position","endPosition","relevant","compare","nextEntry","nextUncompressedPosition","Infinity","lowerBound","upperBound","searchPosition","floor","comparison","ceil","BgzFilehandle","gziFilehandle","gziPath","gzi","stat","compressedStat","assign","size","getUncompressedFileSize","blocks","blksize","bytesRead","readUInt32LE","_readAndUncompressBlock","blockBuffer","nextCompressedPosition","blockCompressedLength","blockPositions","destinationOffset","blockNum","uncompressedBuffer","sourceOffset","sourceEnd","copy"],"sourceRoot":""}