Mercurial > repos > fubar > jbrowse2
view 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
| author | fubar |
|---|---|
| date | Sat, 05 Oct 2024 23:58:05 +0000 |
| parents | |
| children |
line wrap: on
line source
{"version":3,"file":"static/js/4284.61dbc58f.chunk.js","mappings":"2MAOe,MAAMA,UAAwBC,EAAAA,YAC3C,aAAMC,GACJ,MAAMC,EAAKC,KAAKC,cACVC,EAAMF,KAAKG,QAAQ,oBACzB,GAAgB,KAAZD,EAAIE,KAA0B,6BAAZF,EAAIE,IACxB,MAAO,GAET,MAAMC,QAAeC,EAAAA,EAAAA,cAAaJ,EAAKH,GAAIQ,WACrCC,GAAMC,EAAAA,EAAAA,QAAOJ,SAAgBK,EAAAA,EAAAA,OAAML,GAAUA,EAEnD,OADa,IAAIM,YAAY,OAAQ,CAAEC,OAAO,IAAQC,OAAOL,GAE1DM,MAAM,cACNC,QAAOC,KAAOA,EAAEC,SAChBC,KAAI,CAACC,EAAMC,KACV,MAAOC,EAASC,EAAOC,EAAKC,EAAMC,GAAQN,EAAKL,MAAM,MACrD,OAAO,IAAIY,EAAAA,cAAc,CACvBC,SAAU,GAAGP,IACbC,QAASA,EACTC,OAAQA,EACRC,KAAMA,EACNC,KAAMA,EACNC,KAAMA,GACN,GAER,CAEAG,aAAAA,GAAuC,E,6FChBzCC,eAAenB,EAAMoB,GACnB,IACE,IAAIC,EACAC,EAAM,EACNZ,EAAI,EACR,MAAMa,EAAS,GACf,IACIC,EADAC,EAAY,EAEhB,EAAG,CACD,MAAMC,EAAiBN,EAAUO,SAASL,GAK1C,GAJAE,EAAW,IAAI,EAAAI,UAEXP,QAASG,GACbA,EAASK,KAAKH,EAAgB,EAAAI,cAC1BN,EAASO,IACX,MAAM,IAAIC,MAAMR,EAASS,KAG3BX,GAAOD,EAAKa,QACZX,EAAOb,GAAKc,EAASW,OACrBV,GAAaF,EAAOb,GAAG0B,OACvB1B,GAAK,C,OACEW,EAAKgB,UAEd,MAAMF,EAAS,IAAIG,WAAWb,GAC9B,IAAK,IAAIf,EAAI,EAAG6B,EAAS,EAAG7B,EAAIa,EAAOa,OAAQ1B,IAC7CyB,EAAOK,IAAIjB,EAAOb,GAAI6B,GACtBA,GAAUhB,EAAOb,GAAG0B,OAEtB,OAAO,KAAOK,KAAKN,E,CACnB,MAAOO,GAEP,GAAI,GAAGA,IAAIC,MAAM,0BACf,MAAM,IAAIX,MACR,4DAGJ,MAAMU,C,CAEV,CAgDAvB,eAAeyB,EAAgBxB,EAAmByB,GAChD,IACE,IAAIxB,EACJ,MAAM,KAAEyB,EAAI,KAAEC,GAASF,EACvB,IAAIG,EAAOF,EAAKG,cACZC,EAAOJ,EAAKK,aAChB,MAAM5B,EAAS,GACT6B,EAAa,GACbC,EAAa,GAEnB,IAAI5B,EAAY,EACZf,EAAI,EACR,EAAG,CACD,MAAMgB,EAAiBN,EAAUO,SAASqB,EAAOF,EAAKG,eAChDzB,EAAW,IAAI,EAAAI,QAIrB,KAFIP,QAASG,GACbA,EAASK,KAAKH,EAAgB,EAAAI,cAC1BN,EAASO,IACX,MAAM,IAAIC,MAAMR,EAASS,KAG3B,MAAMtC,EAAS6B,EAASW,OACxBZ,EAAOM,KAAKlC,GACZ,IAAI2D,EAAM3D,EAAOyC,OAEjBgB,EAAWvB,KAAKmB,GAChBK,EAAWxB,KAAKqB,GACM,IAAlB3B,EAAOa,QAAgBU,EAAKK,eAE9B5B,EAAO,GAAKA,EAAO,GAAGI,SAASmB,EAAKK,cACpCG,EAAM/B,EAAO,GAAGa,QAElB,MAAMmB,EAAWP,EAIjB,GAHAA,GAAQ3B,EAAKa,QACbgB,GAAQI,EAEJC,GAAYR,EAAKE,cAAe,CAKlC1B,EAAOb,GAAKa,EAAOb,GAAGiB,SACpB,EACAoB,EAAKE,gBAAkBH,EAAKG,cACxBF,EAAKI,aAAeL,EAAKK,aAAe,EACxCJ,EAAKI,aAAe,GAG1BC,EAAWvB,KAAKmB,GAChBK,EAAWxB,KAAKqB,GAChBzB,GAAaF,EAAOb,GAAG0B,OACvB,K,CAEFX,GAAaF,EAAOb,GAAG0B,OACvB1B,G,OACOW,EAAKgB,UAEd,MAAMF,EAAS,IAAIG,WAAWb,GAC9B,IAAK,IAAIf,EAAI,EAAG6B,EAAS,EAAG7B,EAAIa,EAAOa,OAAQ1B,IAC7CyB,EAAOK,IAAIjB,EAAOb,GAAI6B,GACtBA,GAAUhB,EAAOb,GAAG0B,OAItB,MAAO,CAAEzC,OAFM,KAAO8C,KAAKN,GAEViB,aAAYC,a,CAC7B,MAAOX,GAEP,GAAI,GAAGA,IAAIC,MAAM,0BACf,MAAM,IAAIX,MACR,4DAGJ,MAAMU,C,CAEV,C,wBC5Ke,MAAMc,EAKnB,WAAAC,EAAY,WACVC,EAAU,KACVC,IAKA,GAAID,EACFpE,KAAKoE,WAAaA,MACb,KAAIC,EAGT,MAAM,IAAIC,UAAU,6CAFpBtE,KAAKoE,WAAa,IAAI,KAAUC,E,CAIpC,CAEA,qBAAAE,CAAsB/D,EAAayC,EAAS,EAAGuB,GAAW,GAExD,MAAMC,EAAO,gBAAiBjE,EAAIkE,MAAMzB,EAAQA,EAAS,GAAIuB,GAC7D,GACEC,EAAKE,YAAYC,OAAOC,mBACxBJ,EAAKK,SAASF,OAAOG,kBAErB,MAAM,IAAIT,UAAU,oBAGtB,OAAOG,EAAKO,UACd,CAEA,SAAAC,GAIE,OAHKjF,KAAKkF,QACRlF,KAAKkF,MAAQlF,KAAKmF,cAEbnF,KAAKkF,KACd,CAEA,gBAAMC,GACJ,IAAI3E,EAAM,KAAO4E,YAAY,SACvBpF,KAAKoE,WAAWiB,KAAK7E,EAAK,EAAG,EAAG,GACtC,MAAM8E,EAAatF,KAAKuE,sBAAsB/D,EAAK,GAAG,GACtD,IAAK8E,EACH,MAAO,CAAC,CAAC,EAAG,IAGd,MAAMC,EAAU,IAAIC,MAAMF,EAAa,GACvCC,EAAQ,GAAK,CAAC,EAAG,GAGjB,MAAME,EAAU,GAAQH,EACxB,GAAIG,EAAUb,OAAOC,iBACnB,MAAM,IAAIP,UAAU,oBAEtB9D,EAAM,KAAO4E,YAAYK,SACnBzF,KAAKoE,WAAWiB,KAAK7E,EAAK,EAAGiF,EAAS,GAC5C,IAAK,IAAIC,EAAc,EAAGA,EAAcJ,EAAYI,GAAe,EAAG,CACpE,MAAMC,EAAqB3F,KAAKuE,sBAC9B/D,EACc,GAAdkF,GAEIE,EAAuB5F,KAAKuE,sBAChC/D,EACc,GAAdkF,EAAmB,GAErBH,EAAQG,EAAc,GAAK,CAACC,EAAoBC,E,CAGlD,OAAOL,CACT,CAEA,kBAAMM,GACJ,MAAMN,QAAgBvF,KAAKiF,YAC3B,GAAKM,EAAQzC,OAGb,OAAOyC,EAAQA,EAAQzC,OAAS,EAClC,CAEA,8BAAMgD,CAAyBhD,EAAgBiD,GAC7C,MAAMC,EAAcD,EAAWjD,EAC/B,GAAe,IAAXA,EACF,MAAO,GAET,MAAMyC,QAAgBvF,KAAKiF,YACrBgB,EAAW,GAIXC,EAAU,CAACC,EAAYC,KAC3B,MAAMR,EAAuBO,EA/FL,GAgGlBE,EAA2BD,EAC7BA,EAjGoB,GAkGpBE,IAEJ,OACEV,GAAwBG,GACxBM,EAA2BN,EAEpB,EAGLH,EAAuBG,GACjB,EAGH,CAAC,EAGV,IAAIQ,EAAa,EACbC,EAAajB,EAAQzC,OAAS,EAC9B2D,EAAiBC,KAAKC,MAAMpB,EAAQzC,OAAS,GAE7C8D,EAAaV,EACfX,EAAQkB,GACRlB,EAAQkB,EAAiB,IAE3B,KAAsB,IAAfG,GACDA,EAAa,EACfJ,EAAaC,EAAiB,EACrBG,EAAa,IACtBL,EAAaE,EAAiB,GAEhCA,EAAiBC,KAAKG,MAAML,EAAaD,GAAc,GAAKA,EAC5DK,EAAaV,EAAQX,EAAQkB,GAAiBlB,EAAQkB,EAAiB,IAIzER,EAAS1D,KAAKgD,EAAQkB,IACtB,IAAIrF,EAAIqF,EAAiB,EACzB,KAAOrF,EAAImE,EAAQzC,SACjBmD,EAAS1D,KAAKgD,EAAQnE,MAClBmE,EAAQnE,GAzIY,IAyIiB4E,IAFhB5E,GAAK,GAShC,OAHI6E,EAASA,EAASnD,OAAS,GA7IL,GA6IiCkD,GACzDC,EAAS1D,KAAK,IAET0D,CACT,EC/Ia,MAAMa,EAInB,WAAA3C,EAAY,WACVC,EAAU,KACVC,EAAI,cACJ0C,EAAa,QACbC,IAOA,GAAI5C,EACFpE,KAAKoE,WAAaA,MACb,KAAIC,EAGT,MAAM,IAAIC,UAAU,6CAFpBtE,KAAKoE,WAAa,IAAI,KAAUC,E,CAKlC,IAAK0C,IAAkBC,IAAY3C,EACjC,MAAM,IAAIC,UAAU,mDAGtBtE,KAAKiH,IAAM,IAAI/C,EAAS,CACtBE,WAAY2C,EACZ1C,KAAO0C,GAAkBC,IAAW3C,EAAiB,GAAGA,QAAb2C,GAE/C,CAEA,UAAME,GACJ,MAAMC,QAAuBnH,KAAKoE,WAAW8C,OAC7C,OAAOE,OAAOC,OAAOF,EAAgB,CACnCG,WAAYtH,KAAKuH,0BACjBC,YAAQC,EACRC,aAASD,GAEb,CAEA,6BAAMF,GAGJ,MAAO,CAAE3B,SAA8B5F,KAAKiH,IAAIpB,gBAE1C,KAAEyB,SAAetH,KAAKoE,WAAW8C,OAEjC1G,EAAM,KAAO4E,YAAY,IAGzB,UAAEuC,SAAoB3H,KAAKoE,WAAWiB,KAAK7E,EAAK,EAAG,EAAG8G,EAAO,GAAK,GACxE,GAAkB,IAAdK,EACF,MAAM,IAAIjF,MAAM,cAGlB,OAAOkD,EAD2BpF,EAAIoH,aAAa,EAErD,CAEA,6BAAMC,CACJC,GACCnC,IACAoC,IAED,IAAIC,EAAOD,EACNC,IACHA,SAAchI,KAAKoE,WAAW8C,QAAQI,MAIxC,MAAMW,EAAwBD,EAAOrC,EAcrC,aAZM3F,KAAKoE,WAAWiB,KACpByC,EACA,EACAG,EACAtC,SAI2BjF,EAC3BoH,EAAYpD,MAAM,EAAGuD,GAIzB,CAEA,UAAM5C,CAAK7E,EAAayC,EAAgBH,EAAgBiD,GAEtD,MAAMmC,QAAuBlI,KAAKiH,IAAInB,yBACpChD,EACAiD,GAEI+B,EAAc,KAAO1C,YAAY,OAEvC,IAAI+C,EAAoBlF,EACpB0E,EAAY,EAChB,IACE,IAAIS,EAAW,EACfA,EAAWF,EAAepF,OAAS,EACnCsF,GAAY,EACZ,CAEA,MAAMC,QAA2BrI,KAAK6H,wBACpCC,EACAI,EAAeE,GACfF,EAAeE,EAAW,KAErB,CAAExC,GAAwBsC,EAAeE,GAC1CE,EACJ1C,GAAwBG,EAAW,EAAIA,EAAWH,EAC9C2C,EACJ7B,KAAK8B,IACHzC,EAAWjD,EACX8C,EAAuByC,EAAmBvF,QACxC8C,EACF0C,GAAgB,GAAKA,EAAeD,EAAmBvF,SACzDuF,EAAmBI,KAAKjI,EAAK2H,EAAmBG,EAAcC,GAC9DJ,GAAqBI,EAAYD,EACjCX,GAAaY,EAAYD,E,CAI7B,MAAO,CAAEX,YAAWtH,OAAQG,EAC9B,E","sources":["../../../packages/core/data_adapters/CytobandAdapter/CytobandAdapter.ts","../../../node_modules/@gmod/bgzf-filehandle/src/unzip-pako.ts","../../../node_modules/@gmod/bgzf-filehandle/src/gziIndex.ts","../../../node_modules/@gmod/bgzf-filehandle/src/bgzFilehandle.ts"],"sourcesContent":["import { 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":""}