jbrowse2: x/static/js/2977.aa562b03.chunk.js.map annotate

annotate x/static/js/2977.aa562b03.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

rev	line source
125 49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566 fubar parents: diff changeset	1 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NullSignal {}\n\n/*\n aggregates a number of abort signals, will only fire the aggregated\n * abort if all of the input signals have been aborted\n /\nexport default class AggregateAbortController {\n signals = new Set()\n abortController = new AbortController()\n\n /\n @param {AbortSignal} [signal] optional AbortSignal to add. if falsy,\n * will be treated as a null-signal, and this abortcontroller will no\n * longer be abortable.\n /\n //@ts-ignore\n addSignal(signal: AbortSignal = new NullSignal()): void {\n if (this.signal.aborted) {\n throw new Error('cannot add a signal, already aborted!')\n }\n\n // note that a NullSignal will never fire, so if we\n // have one this thing will never actually abort\n this.signals.add(signal)\n if (signal.aborted) {\n // handle the abort immediately if it is already aborted\n // for some reason\n this.handleAborted(signal)\n } else if (typeof signal.addEventListener === 'function') {\n signal.addEventListener('abort', () => {\n this.handleAborted(signal)\n })\n }\n }\n\n handleAborted(signal: AbortSignal): void {\n this.signals.delete(signal)\n if (this.signals.size === 0) {\n this.abortController.abort()\n }\n }\n\n get signal(): AbortSignal {\n return this.abortController.signal\n }\n\n abort(): void {\n this.abortController.abort()\n }\n}\n","export default class AggregateStatusReporter {\n callbacks = new Set<Function>()\n currentMessage: unknown\n\n addCallback(callback: Function = () => {}): void {\n this.callbacks.add(callback)\n callback(this.currentMessage)\n }\n\n callback(message: unknown) {\n this.currentMessage = message\n for (const elt of this.callbacks) {\n elt(message)\n }\n }\n}\n","import AggregateAbortController from './AggregateAbortController'\nimport AggregateStatusReporter from './AggregateStatusReporter'\n\ninterface Cache<U> {\n delete: (key: string) => void\n keys: () => Iterator<string>\n get: (key: string) => U \| undefined\n set: (key: string, value: U) => void\n has: (key: string) => boolean\n}\ntype FillCallback<T, U> = (\n data: T,\n signal?: AbortSignal,\n statusCallback?: Function,\n) => Promise<U>\n\ninterface Entry<U> {\n aborter: AggregateAbortController\n settled: boolean\n readonly aborted: boolean\n statusReporter: AggregateStatusReporter\n promise: Promise<U>\n}\nexport default class AbortablePromiseCache<T, U> {\n /\n @param {object} args constructor args\n * @param {Function} args.fill fill callback, will be called with sig `fill(data, signal)`\n * @param {object} args.cache backing store to use, must implement `get(key)`, `set(key, val)`,\n * `delete(key)`, and `keys() -> iterator`\n /\n\n private cache: Cache<Entry<U>>\n private fillCallback: FillCallback<T, U>\n\n constructor({\n fill,\n cache,\n }: {\n fill: FillCallback<T, U>\n cache: Cache<Entry<U>>\n }) {\n if (typeof fill !== 'function') {\n throw new TypeError('must pass a fill function')\n }\n if (typeof cache !== 'object') {\n throw new TypeError('must pass a cache object')\n }\n if (\n typeof cache.get !== 'function' \|\|\n typeof cache.set !== 'function' \|\|\n typeof cache.delete !== 'function'\n ) {\n throw new TypeError(\n 'cache must implement get(key), set(key, val), and and delete(key)',\n )\n }\n\n this.cache = cache\n this.fillCallback = fill\n }\n\n static isAbortException(exception: Error) {\n return (\n // DOMException\n exception.name === 'AbortError' \|\|\n // standard-ish non-DOM abort exception\n //@ts-ignore\n exception.code === 'ERR_ABORTED' \|\|\n // stringified DOMException\n exception.message === 'AbortError: aborted' \|\|\n // stringified standard-ish exception\n exception.message === 'Error: aborted'\n )\n }\n\n evict(key: string, entry: Entry<U>) {\n if (this.cache.get(key) === entry) {\n this.cache.delete(key)\n }\n }\n\n fill(key: string, data: T, signal?: AbortSignal, statusCallback?: Function) {\n const aborter = new AggregateAbortController()\n const statusReporter = new AggregateStatusReporter()\n statusReporter.addCallback(statusCallback)\n const newEntry: Entry<U> = {\n aborter: aborter,\n promise: this.fillCallback(data, aborter.signal, (message: unknown) => {\n statusReporter.callback(message)\n }),\n settled: false,\n statusReporter,\n get aborted() {\n return this.aborter.signal.aborted\n },\n }\n newEntry.aborter.addSignal(signal)\n\n // remove the fill from the cache when its abortcontroller fires, if still in there\n newEntry.aborter.signal.addEventListener('abort', () => {\n if (!newEntry.settled) {\n this.evict(key, newEntry)\n }\n })\n\n // chain off the cached promise to record when it settles\n newEntry.promise\n .then(\n () => {\n newEntry.settled = true\n },\n () => {\n newEntry.settled = true\n\n // if the fill throws an error (including abort) and is still in the cache, remove it\n this.evict(key, newEntry)\n },\n )\n .catch(error => {\n // this will only be reached if there is some kind of\n // bad bug in this library\n console.error(error)\n throw error\n })\n\n this.cache.set(key, newEntry)\n }\n\n static checkSinglePromise<U>(promise: Promise<U>, signal?: AbortSignal) {\n // check just this signal for having been aborted, and abort the\n // promise if it was, regardless of what happened with the cached\n // response\n function checkForSingleAbort() {\n if (signal?.aborted) {\n throw Object.assign(new Error('aborted'), { code: 'ERR_ABORTED' })\n }\n }\n\n return promise.then(\n result => {\n checkForSingleAbort()\n return result\n },\n error => {\n checkForSingleAbort()\n throw error\n },\n )\n }\n\n has(key: string): boolean {\n return this.cache.has(key)\n }\n\n /\n Callback for getting status of the pending async\n \n @callback statusCallback\n * @param {any} status, current status string or message object\n /\n\n /\n @param {any} key cache key to use for this request\n * @param {any} data data passed as the first argument to the fill callback\n * @param {AbortSignal} [signal] optional AbortSignal object that aborts the request\n * @param {statusCallback} a callback to get the current status of a pending async operation\n /\n get(\n key: string,\n data: T,\n signal?: AbortSignal,\n statusCallback?: Function,\n ): Promise<U> {\n if (!signal && data instanceof AbortSignal) {\n throw new TypeError(\n 'second get argument appears to be an AbortSignal, perhaps you meant to pass `null` for the fill data?',\n )\n }\n const cacheEntry = this.cache.get(key)\n\n if (cacheEntry) {\n if (cacheEntry.aborted && !cacheEntry.settled) {\n // if it's aborted but has not realized it yet, evict it and redispatch\n this.evict(key, cacheEntry)\n return this.get(key, data, signal, statusCallback)\n }\n\n if (cacheEntry.settled) {\n // too late to abort, just return it\n return cacheEntry.promise\n }\n\n // request is in-flight, add this signal to its list of signals,\n // or if there is no signal, the aborter will become non-abortable\n cacheEntry.aborter.addSignal(signal)\n cacheEntry.statusReporter.addCallback(statusCallback)\n\n return AbortablePromiseCache.checkSinglePromise(\n cacheEntry.promise,\n signal,\n )\n }\n\n // if we got here, it is not in the cache. fill.\n this.fill(key, data, signal, statusCallback)\n return AbortablePromiseCache.checkSinglePromise(\n //see https://www.typescriptlang.org/docs/handbook/2/everyday-types.html#non-null-assertion-operator-postfix-\n\n this.cache.get(key)!.promise,\n signal,\n )\n }\n\n /\n delete the given entry from the cache. if it exists and its fill request has\n * not yet settled, the fill will be signaled to abort.\n \n @param {any} key\n /\n delete(key: string) {\n const cachedEntry = this.cache.get(key)\n if (cachedEntry) {\n if (!cachedEntry.settled) {\n cachedEntry.aborter.abort()\n }\n this.cache.delete(key)\n }\n }\n\n /\n Clear all requests from the cache. Aborts any that have not settled.\n * @returns {number} count of entries deleted\n /\n clear() {\n // iterate without needing regenerator-runtime\n const keyIter = this.cache.keys()\n let deleteCount = 0\n for (let result = keyIter.next(); !result.done; result = keyIter.next()) {\n this.delete(result.value)\n deleteCount += 1\n }\n return deleteCount\n }\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","import { LocalFile, GenericFilehandle } from 'generic-filehandle'\nimport { Buffer } from 'buffer'\n\ninterface BaseOpts {\n signal?: AbortSignal\n}\n\ninterface IndexEntry {\n offset: number\n lineBytes: number\n lineLength: number\n length: number\n}\n\nfunction _faiOffset(idx: IndexEntry, pos: number) {\n return (\n idx.offset +\n idx.lineBytes * Math.floor(pos / idx.lineLength) +\n (pos % idx.lineLength)\n )\n}\n\nasync function readFAI(fai: GenericFilehandle, opts?: BaseOpts) {\n const text = await fai.readFile(opts)\n if (!text?.length) {\n throw new Error('No data read from FASTA index (FAI) file')\n }\n\n let idCounter = 0\n let currSeq: { name: string; id: number } \| undefined\n const data = text\n .toString('utf8')\n .split(/\\r?\\n/)\n .filter(line => /\\S/.test(line))\n .map(line => line.split('\\t'))\n .filter(row => row[0] !== '')\n .map(row => {\n if (!currSeq \|\| currSeq.name !== row[0]) {\n currSeq = { name: row[0], id: idCounter }\n idCounter += 1\n }\n\n return {\n id: currSeq.id,\n name: row[0],\n length: +row[1],\n start: 0,\n end: +row[1],\n offset: +row[2],\n lineLength: +row[3],\n lineBytes: +row[4],\n }\n })\n\n return {\n name: Object.fromEntries(data.map(entry => [entry.name, entry])),\n id: Object.fromEntries(data.map(entry => [entry.id, entry])),\n }\n}\n\nexport default class IndexedFasta {\n fasta: GenericFilehandle\n fai: GenericFilehandle\n indexes?: ReturnType<typeof readFAI>\n\n constructor({\n fasta,\n fai,\n path,\n faiPath,\n }: {\n fasta?: GenericFilehandle\n fai?: GenericFilehandle\n path?: string\n faiPath?: string\n }) {\n if (fasta) {\n this.fasta = fasta\n } else if (path) {\n this.fasta = new LocalFile(path)\n } else {\n throw new Error('Need to pass filehandle for fasta or path to localfile')\n }\n\n if (fai) {\n this.fai = fai\n } else if (faiPath) {\n this.fai = new LocalFile(faiPath)\n } else if (path) {\n this.fai = new LocalFile(`${path}.fai`)\n } else {\n throw new Error('Need to pass filehandle for or path to localfile')\n }\n }\n\n async _getIndexes(opts?: BaseOpts) {\n if (!this.indexes) {\n this.indexes = readFAI(this.fai, opts)\n }\n return this.indexes\n }\n\n /*\n @returns {array[string]} array of string sequence\n * names that are present in the index, in which the\n * array index indicates the sequence ID, and the value\n * is the sequence name\n /\n async getSequenceNames(opts?: BaseOpts) {\n return Object.keys((await this._getIndexes(opts)).name)\n }\n\n /\n @returns {array[string]} array of string sequence\n * names that are present in the index, in which the\n * array index indicates the sequence ID, and the value\n * is the sequence name\n /\n async getSequenceSizes(opts?: BaseOpts) {\n const returnObject = {} as Record<string, number>\n const idx = await this._getIndexes(opts)\n for (const val of Object.values(idx.id)) {\n returnObject[val.name] = val.length\n }\n return returnObject\n }\n\n /\n @returns {array[string]} array of string sequence\n * names that are present in the index, in which the\n * array index indicates the sequence ID, and the value\n * is the sequence name\n /\n async getSequenceSize(seqName: string, opts?: BaseOpts) {\n const idx = await this._getIndexes(opts)\n return idx.name[seqName]?.length\n }\n\n /\n \n * @param {string} name\n * @returns {Promise[boolean]} true if the file contains the given reference sequence name\n /\n async hasReferenceSequence(name: string, opts?: BaseOpts) {\n return !!(await this._getIndexes(opts)).name[name]\n }\n\n /\n \n * @param {number} seqId\n * @param {number} min\n * @param {number} max\n /\n async getResiduesById(\n seqId: number,\n min: number,\n max: number,\n opts?: BaseOpts,\n ) {\n const indexEntry = (await this._getIndexes(opts)).id[seqId]\n if (!indexEntry) {\n return undefined\n }\n return this._fetchFromIndexEntry(indexEntry, min, max, opts)\n }\n\n /\n @param {string} seqName\n * @param {number} min\n * @param {number} max\n */\n async getResiduesByName(\n seqName: string,\n min: number,\n max: number,\n opts?: BaseOpts,\n ) {\n const indexEntry = (await this._getIndexes(opts)).name[seqName]\n if (!indexEntry) {\n return undefined\n }\n\n return this._fetchFromIndexEntry(indexEntry, min, max, opts)\n }\n\n //alias for getResiduesByName\n async getSequence(\n seqName: string,\n min: number,\n max: number,\n opts?: BaseOpts,\n ) {\n return this.getResiduesByName(seqName, min, max, opts)\n }\n\n async _fetchFromIndexEntry(\n indexEntry: IndexEntry,\n min = 0,\n max: number,\n opts?: BaseOpts,\n ) {\n let end = max\n if (min < 0) {\n throw new TypeError('regionStart cannot be less than 0')\n }\n if (end === undefined \|\| end > indexEntry.length) {\n end = indexEntry.length\n }\n if (min >= end) {\n return ''\n }\n\n const position = _faiOffset(indexEntry, min)\n const readlen = _faiOffset(indexEntry, end) - position\n\n const residues = Buffer.allocUnsafe(readlen)\n await this.fasta.read(residues, 0, readlen, position, opts)\n return residues.toString('utf8').replace(/\\s+/g, '')\n }\n}\n","import { BgzfFilehandle } from '@gmod/bgzf-filehandle'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport IndexedFasta from './indexedFasta'\n\nexport default class BgzipIndexedFasta extends IndexedFasta {\n constructor({\n fasta,\n path,\n fai,\n faiPath,\n gzi,\n gziPath,\n }: {\n fasta?: GenericFilehandle\n path?: string\n fai?: GenericFilehandle\n faiPath?: string\n gzi?: GenericFilehandle\n gziPath?: string\n }) {\n super({ fasta, path, fai, faiPath })\n if (fasta && gzi) {\n // @ts-expect-error\n this.fasta = new BgzfFilehandle({\n filehandle: fasta,\n gziFilehandle: gzi,\n })\n } else if (path && gziPath) {\n // @ts-expect-error\n this.fasta = new BgzfFilehandle({ path, gziPath })\n }\n }\n}\n"],"names":["NullSignal","AggregateAbortController","signals","Set","abortController","AbortController","addSignal","signal","this","aborted","Error","add","handleAborted","addEventListener","delete","size","abort","AggregateStatusReporter","callbacks","addCallback","callback","currentMessage","message","elt","AbortablePromiseCache","constructor","fill","cache","TypeError","get","set","fillCallback","isAbortException","exception","name","code","evict","key","entry","data","statusCallback","aborter","statusReporter","newEntry","promise","settled","then","catch","error","console","checkSinglePromise","checkForSingleAbort","Object","assign","result","has","AbortSignal","cacheEntry","cachedEntry","clear","keyIter","keys","deleteCount","next","done","value","async","unzip","inputData","strm","pos","i","chunks","inflator","totalSize","remainingInput","subarray","Inflate","push","Z_SYNC_FLUSH","err","msg","next_in","length","avail_in","Uint8Array","offset","from","e","match","unzipChunkSlice","chunk","minv","maxv","cpos","blockPosition","dpos","dataPosition","cpositions","dpositions","buffer","len","origCpos","GziIndex","filehandle","path","_readLongWithOverflow","buf","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","nextEntry","nextUncompressedPosition","Infinity","lowerBound","upperBound","searchPosition","Math","floor","comparison","ceil","BgzFilehandle","gziFilehandle","gziPath","gzi","stat","compressedStat","getUncompressedFileSize","blocks","undefined","blksize","bytesRead","readUInt32LE","_readAndUncompressBlock","blockBuffer","nextCompressedPosition","blockCompressedLength","blockPositions","destinationOffset","blockNum","uncompressedBuffer","sourceOffset","sourceEnd","min","copy","_faiOffset","idx","lineBytes","lineLength","IndexedFasta","fasta","fai","faiPath","_getIndexes","opts","indexes","text","readFile","currSeq","idCounter","toString","split","filter","line","test","map","row","id","start","end","fromEntries","readFAI","getSequenceNames","getSequenceSizes","returnObject","val","values","getSequenceSize","seqName","hasReferenceSequence","getResiduesById","seqId","max","indexEntry","_fetchFromIndexEntry","getResiduesByName","getSequence","readlen","residues","replace","BgzipIndexedFasta","super"],"sourceRoot":""}

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49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

fubar

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NullSignal {}\n\n/**\n * aggregates a number of abort signals, will only fire the aggregated\n * abort if all of the input signals have been aborted\n */\nexport default class AggregateAbortController {\n signals = new Set()\n abortController = new AbortController()\n\n /**\n * @param {AbortSignal} [signal] optional AbortSignal to add. if falsy,\n * will be treated as a null-signal, and this abortcontroller will no\n * longer be abortable.\n */\n //@ts-ignore\n addSignal(signal: AbortSignal = new NullSignal()): void {\n if (this.signal.aborted) {\n throw new Error('cannot add a signal, already aborted!')\n }\n\n // note that a NullSignal will never fire, so if we\n // have one this thing will never actually abort\n this.signals.add(signal)\n if (signal.aborted) {\n // handle the abort immediately if it is already aborted\n // for some reason\n this.handleAborted(signal)\n } else if (typeof signal.addEventListener === 'function') {\n signal.addEventListener('abort', () => {\n this.handleAborted(signal)\n })\n }\n }\n\n handleAborted(signal: AbortSignal): void {\n this.signals.delete(signal)\n if (this.signals.size === 0) {\n this.abortController.abort()\n }\n }\n\n get signal(): AbortSignal {\n return this.abortController.signal\n }\n\n abort(): void {\n this.abortController.abort()\n }\n}\n","export default class AggregateStatusReporter {\n callbacks = new Set<Function>()\n currentMessage: unknown\n\n addCallback(callback: Function = () => {}): void {\n this.callbacks.add(callback)\n callback(this.currentMessage)\n }\n\n callback(message: unknown) {\n this.currentMessage = message\n for (const elt of this.callbacks) {\n elt(message)\n }\n }\n}\n","import AggregateAbortController from './AggregateAbortController'\nimport AggregateStatusReporter from './AggregateStatusReporter'\n\ninterface Cache {\n delete: (key: string) => void\n keys: () => Iterator<string>\n get: (key: string) => U | undefined\n set: (key: string, value: U) => void\n has: (key: string) => boolean\n}\ntype FillCallback<T, U> = (\n data: T,\n signal?: AbortSignal,\n statusCallback?: Function,\n) => Promise\n\ninterface Entry {\n aborter: AggregateAbortController\n settled: boolean\n readonly aborted: boolean\n statusReporter: AggregateStatusReporter\n promise: Promise\n}\nexport default class AbortablePromiseCache<T, U> {\n /**\n * @param {object} args constructor args\n * @param {Function} args.fill fill callback, will be called with sig `fill(data, signal)`\n * @param {object} args.cache backing store to use, must implement `get(key)`, `set(key, val)`,\n * `delete(key)`, and `keys() -> iterator`\n */\n\n private cache: Cache<Entry>\n private fillCallback: FillCallback<T, U>\n\n constructor({\n fill,\n cache,\n }: {\n fill: FillCallback<T, U>\n cache: Cache<Entry>\n }) {\n if (typeof fill !== 'function') {\n throw new TypeError('must pass a fill function')\n }\n if (typeof cache !== 'object') {\n throw new TypeError('must pass a cache object')\n }\n if (\n typeof cache.get !== 'function' ||\n typeof cache.set !== 'function' ||\n typeof cache.delete !== 'function'\n ) {\n throw new TypeError(\n 'cache must implement get(key), set(key, val), and and delete(key)',\n )\n }\n\n this.cache = cache\n this.fillCallback = fill\n }\n\n static isAbortException(exception: Error) {\n return (\n // DOMException\n exception.name === 'AbortError' ||\n // standard-ish non-DOM abort exception\n //@ts-ignore\n exception.code === 'ERR_ABORTED' ||\n // stringified DOMException\n exception.message === 'AbortError: aborted' ||\n // stringified standard-ish exception\n exception.message === 'Error: aborted'\n )\n }\n\n evict(key: string, entry: Entry) {\n if (this.cache.get(key) === entry) {\n this.cache.delete(key)\n }\n }\n\n fill(key: string, data: T, signal?: AbortSignal, statusCallback?: Function) {\n const aborter = new AggregateAbortController()\n const statusReporter = new AggregateStatusReporter()\n statusReporter.addCallback(statusCallback)\n const newEntry: Entry = {\n aborter: aborter,\n promise: this.fillCallback(data, aborter.signal, (message: unknown) => {\n statusReporter.callback(message)\n }),\n settled: false,\n statusReporter,\n get aborted() {\n return this.aborter.signal.aborted\n },\n }\n newEntry.aborter.addSignal(signal)\n\n // remove the fill from the cache when its abortcontroller fires, if still in there\n newEntry.aborter.signal.addEventListener('abort', () => {\n if (!newEntry.settled) {\n this.evict(key, newEntry)\n }\n })\n\n // chain off the cached promise to record when it settles\n newEntry.promise\n .then(\n () => {\n newEntry.settled = true\n },\n () => {\n newEntry.settled = true\n\n // if the fill throws an error (including abort) and is still in the cache, remove it\n this.evict(key, newEntry)\n },\n )\n .catch(error => {\n // this will only be reached if there is some kind of\n // bad bug in this library\n console.error(error)\n throw error\n })\n\n this.cache.set(key, newEntry)\n }\n\n static checkSinglePromise(promise: Promise, signal?: AbortSignal) {\n // check just this signal for having been aborted, and abort the\n // promise if it was, regardless of what happened with the cached\n // response\n function checkForSingleAbort() {\n if (signal?.aborted) {\n throw Object.assign(new Error('aborted'), { code: 'ERR_ABORTED' })\n }\n }\n\n return promise.then(\n result => {\n checkForSingleAbort()\n return result\n },\n error => {\n checkForSingleAbort()\n throw error\n },\n )\n }\n\n has(key: string): boolean {\n return this.cache.has(key)\n }\n\n /**\n * Callback for getting status of the pending async\n *\n * @callback statusCallback\n * @param {any} status, current status string or message object\n */\n\n /**\n * @param {any} key cache key to use for this request\n * @param {any} data data passed as the first argument to the fill callback\n * @param {AbortSignal} [signal] optional AbortSignal object that aborts the request\n * @param {statusCallback} a callback to get the current status of a pending async operation\n */\n get(\n key: string,\n data: T,\n signal?: AbortSignal,\n statusCallback?: Function,\n ): Promise {\n if (!signal && data instanceof AbortSignal) {\n throw new TypeError(\n 'second get argument appears to be an AbortSignal, perhaps you meant to pass `null` for the fill data?',\n )\n }\n const cacheEntry = this.cache.get(key)\n\n if (cacheEntry) {\n if (cacheEntry.aborted && !cacheEntry.settled) {\n // if it's aborted but has not realized it yet, evict it and redispatch\n this.evict(key, cacheEntry)\n return this.get(key, data, signal, statusCallback)\n }\n\n if (cacheEntry.settled) {\n // too late to abort, just return it\n return cacheEntry.promise\n }\n\n // request is in-flight, add this signal to its list of signals,\n // or if there is no signal, the aborter will become non-abortable\n cacheEntry.aborter.addSignal(signal)\n cacheEntry.statusReporter.addCallback(statusCallback)\n\n return AbortablePromiseCache.checkSinglePromise(\n cacheEntry.promise,\n signal,\n )\n }\n\n // if we got here, it is not in the cache. fill.\n this.fill(key, data, signal, statusCallback)\n return AbortablePromiseCache.checkSinglePromise(\n //see https://www.typescriptlang.org/docs/handbook/2/everyday-types.html#non-null-assertion-operator-postfix-\n\n this.cache.get(key)!.promise,\n signal,\n )\n }\n\n /**\n * delete the given entry from the cache. if it exists and its fill request has\n * not yet settled, the fill will be signaled to abort.\n *\n * @param {any} key\n */\n delete(key: string) {\n const cachedEntry = this.cache.get(key)\n if (cachedEntry) {\n if (!cachedEntry.settled) {\n cachedEntry.aborter.abort()\n }\n this.cache.delete(key)\n }\n }\n\n /**\n * Clear all requests from the cache. Aborts any that have not settled.\n * @returns {number} count of entries deleted\n */\n clear() {\n // iterate without needing regenerator-runtime\n const keyIter = this.cache.keys()\n let deleteCount = 0\n for (let result = keyIter.next(); !result.done; result = keyIter.next()) {\n this.delete(result.value)\n deleteCount += 1\n }\n return deleteCount\n }\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","import { LocalFile, GenericFilehandle } from 'generic-filehandle'\nimport { Buffer } from 'buffer'\n\ninterface BaseOpts {\n signal?: AbortSignal\n}\n\ninterface IndexEntry {\n offset: number\n lineBytes: number\n lineLength: number\n length: number\n}\n\nfunction _faiOffset(idx: IndexEntry, pos: number) {\n return (\n idx.offset +\n idx.lineBytes * Math.floor(pos / idx.lineLength) +\n (pos % idx.lineLength)\n )\n}\n\nasync function readFAI(fai: GenericFilehandle, opts?: BaseOpts) {\n const text = await fai.readFile(opts)\n if (!text?.length) {\n throw new Error('No data read from FASTA index (FAI) file')\n }\n\n let idCounter = 0\n let currSeq: { name: string; id: number } | undefined\n const data = text\n .toString('utf8')\n .split(/\\r?\\n/)\n .filter(line => /\\S/.test(line))\n .map(line => line.split('\\t'))\n .filter(row => row[0] !== '')\n .map(row => {\n if (!currSeq || currSeq.name !== row[0]) {\n currSeq = { name: row[0], id: idCounter }\n idCounter += 1\n }\n\n return {\n id: currSeq.id,\n name: row[0],\n length: +row[1],\n start: 0,\n end: +row[1],\n offset: +row[2],\n lineLength: +row[3],\n lineBytes: +row[4],\n }\n })\n\n return {\n name: Object.fromEntries(data.map(entry => [entry.name, entry])),\n id: Object.fromEntries(data.map(entry => [entry.id, entry])),\n }\n}\n\nexport default class IndexedFasta {\n fasta: GenericFilehandle\n fai: GenericFilehandle\n indexes?: ReturnType<typeof readFAI>\n\n constructor({\n fasta,\n fai,\n path,\n faiPath,\n }: {\n fasta?: GenericFilehandle\n fai?: GenericFilehandle\n path?: string\n faiPath?: string\n }) {\n if (fasta) {\n this.fasta = fasta\n } else if (path) {\n this.fasta = new LocalFile(path)\n } else {\n throw new Error('Need to pass filehandle for fasta or path to localfile')\n }\n\n if (fai) {\n this.fai = fai\n } else if (faiPath) {\n this.fai = new LocalFile(faiPath)\n } else if (path) {\n this.fai = new LocalFile(`${path}.fai`)\n } else {\n throw new Error('Need to pass filehandle for or path to localfile')\n }\n }\n\n async _getIndexes(opts?: BaseOpts) {\n if (!this.indexes) {\n this.indexes = readFAI(this.fai, opts)\n }\n return this.indexes\n }\n\n /**\n * @returns {array[string]} array of string sequence\n * names that are present in the index, in which the\n * array index indicates the sequence ID, and the value\n * is the sequence name\n */\n async getSequenceNames(opts?: BaseOpts) {\n return Object.keys((await this._getIndexes(opts)).name)\n }\n\n /**\n * @returns {array[string]} array of string sequence\n * names that are present in the index, in which the\n * array index indicates the sequence ID, and the value\n * is the sequence name\n */\n async getSequenceSizes(opts?: BaseOpts) {\n const returnObject = {} as Record<string, number>\n const idx = await this._getIndexes(opts)\n for (const val of Object.values(idx.id)) {\n returnObject[val.name] = val.length\n }\n return returnObject\n }\n\n /**\n * @returns {array[string]} array of string sequence\n * names that are present in the index, in which the\n * array index indicates the sequence ID, and the value\n * is the sequence name\n */\n async getSequenceSize(seqName: string, opts?: BaseOpts) {\n const idx = await this._getIndexes(opts)\n return idx.name[seqName]?.length\n }\n\n /**\n *\n * @param {string} name\n * @returns {Promise[boolean]} true if the file contains the given reference sequence name\n */\n async hasReferenceSequence(name: string, opts?: BaseOpts) {\n return !!(await this._getIndexes(opts)).name[name]\n }\n\n /**\n *\n * @param {number} seqId\n * @param {number} min\n * @param {number} max\n */\n async getResiduesById(\n seqId: number,\n min: number,\n max: number,\n opts?: BaseOpts,\n ) {\n const indexEntry = (await this._getIndexes(opts)).id[seqId]\n if (!indexEntry) {\n return undefined\n }\n return this._fetchFromIndexEntry(indexEntry, min, max, opts)\n }\n\n /**\n * @param {string} seqName\n * @param {number} min\n * @param {number} max\n */\n async getResiduesByName(\n seqName: string,\n min: number,\n max: number,\n opts?: BaseOpts,\n ) {\n const indexEntry = (await this._getIndexes(opts)).name[seqName]\n if (!indexEntry) {\n return undefined\n }\n\n return this._fetchFromIndexEntry(indexEntry, min, max, opts)\n }\n\n //alias for getResiduesByName\n async getSequence(\n seqName: string,\n min: number,\n max: number,\n opts?: BaseOpts,\n ) {\n return this.getResiduesByName(seqName, min, max, opts)\n }\n\n async _fetchFromIndexEntry(\n indexEntry: IndexEntry,\n min = 0,\n max: number,\n opts?: BaseOpts,\n ) {\n let end = max\n if (min < 0) {\n throw new TypeError('regionStart cannot be less than 0')\n }\n if (end === undefined || end > indexEntry.length) {\n end = indexEntry.length\n }\n if (min >= end) {\n return ''\n }\n\n const position = _faiOffset(indexEntry, min)\n const readlen = _faiOffset(indexEntry, end) - position\n\n const residues = Buffer.allocUnsafe(readlen)\n await this.fasta.read(residues, 0, readlen, position, opts)\n return residues.toString('utf8').replace(/\\s+/g, '')\n }\n}\n","import { BgzfFilehandle } from '@gmod/bgzf-filehandle'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport IndexedFasta from './indexedFasta'\n\nexport default class BgzipIndexedFasta extends IndexedFasta {\n constructor({\n fasta,\n path,\n fai,\n faiPath,\n gzi,\n gziPath,\n }: {\n fasta?: GenericFilehandle\n path?: string\n fai?: GenericFilehandle\n faiPath?: string\n gzi?: GenericFilehandle\n gziPath?: string\n }) {\n super({ fasta, path, fai, faiPath })\n if (fasta && gzi) {\n // @ts-expect-error\n this.fasta = new BgzfFilehandle({\n filehandle: fasta,\n gziFilehandle: gzi,\n })\n } else if (path && gziPath) {\n // @ts-expect-error\n this.fasta = new BgzfFilehandle({ path, gziPath })\n }\n }\n}\n"],"names":["NullSignal","AggregateAbortController","signals","Set","abortController","AbortController","addSignal","signal","this","aborted","Error","add","handleAborted","addEventListener","delete","size","abort","AggregateStatusReporter","callbacks","addCallback","callback","currentMessage","message","elt","AbortablePromiseCache","constructor","fill","cache","TypeError","get","set","fillCallback","isAbortException","exception","name","code","evict","key","entry","data","statusCallback","aborter","statusReporter","newEntry","promise","settled","then","catch","error","console","checkSinglePromise","checkForSingleAbort","Object","assign","result","has","AbortSignal","cacheEntry","cachedEntry","clear","keyIter","keys","deleteCount","next","done","value","async","unzip","inputData","strm","pos","i","chunks","inflator","totalSize","remainingInput","subarray","Inflate","push","Z_SYNC_FLUSH","err","msg","next_in","length","avail_in","Uint8Array","offset","from","e","match","unzipChunkSlice","chunk","minv","maxv","cpos","blockPosition","dpos","dataPosition","cpositions","dpositions","buffer","len","origCpos","GziIndex","filehandle","path","_readLongWithOverflow","buf","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","nextEntry","nextUncompressedPosition","Infinity","lowerBound","upperBound","searchPosition","Math","floor","comparison","ceil","BgzFilehandle","gziFilehandle","gziPath","gzi","stat","compressedStat","getUncompressedFileSize","blocks","undefined","blksize","bytesRead","readUInt32LE","_readAndUncompressBlock","blockBuffer","nextCompressedPosition","blockCompressedLength","blockPositions","destinationOffset","blockNum","uncompressedBuffer","sourceOffset","sourceEnd","min","copy","_faiOffset","idx","lineBytes","lineLength","IndexedFasta","fasta","fai","faiPath","_getIndexes","opts","indexes","text","readFile","currSeq","idCounter","toString","split","filter","line","test","map","row","id","start","end","fromEntries","readFAI","getSequenceNames","getSequenceSizes","returnObject","val","values","getSequenceSize","seqName","hasReferenceSequence","getResiduesById","seqId","max","indexEntry","_fetchFromIndexEntry","getResiduesByName","getSequence","readlen","residues","replace","BgzipIndexedFasta","super"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

annotate x/static/js/2977.aa562b03.chunk.js.map @ 125:49f3d3878413 draft