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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
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rev   line source
125
49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566
fubar
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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 Chunk from './chunk'\nimport VirtualOffset from './virtualOffset'\n\nexport function longToNumber(long: Long) {\n if (\n long.greaterThan(Number.MAX_SAFE_INTEGER) ||\n long.lessThan(Number.MIN_SAFE_INTEGER)\n ) {\n throw new Error('integer overflow')\n }\n return long.toNumber()\n}\n\nclass AbortError extends Error {\n public code: string | undefined\n}\n/**\n * Properly check if the given AbortSignal is aborted. Per the standard, if the\n * signal reads as aborted, this function throws either a DOMException\n * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.\n *\n * For convenience, passing `undefined` is a no-op\n *\n * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`\n * attribute\n *\n * @returns nothing\n */\nexport function checkAbortSignal(signal?: AbortSignal) {\n if (!signal) {\n return\n }\n\n if (signal.aborted) {\n if (typeof DOMException !== 'undefined') {\n throw new DOMException('aborted', 'AbortError')\n } else {\n const e = new AbortError('aborted')\n e.code = 'ERR_ABORTED'\n throw e\n }\n }\n}\n\n/**\n * Skips to the next tick, then runs `checkAbortSignal`.\n * Await this to inside an otherwise synchronous loop to\n * provide a place to break when an abort signal is received.\n * @param {AbortSignal} signal\n */\nexport async function abortBreakPoint(signal?: AbortSignal) {\n await Promise.resolve()\n checkAbortSignal(signal)\n}\n\nexport function canMergeBlocks(chunk1: Chunk, chunk2: Chunk) {\n return (\n chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&\n chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000\n )\n}\n\nexport function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset) {\n const mergedChunks: Chunk[] = []\n let lastChunk: Chunk | null = null\n\n if (chunks.length === 0) {\n return chunks\n }\n\n chunks.sort(function (c0, c1) {\n const dif = c0.minv.blockPosition - c1.minv.blockPosition\n return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition\n })\n\n chunks.forEach(chunk => {\n if (!lowest || chunk.maxv.compareTo(lowest) > 0) {\n if (lastChunk === null) {\n mergedChunks.push(chunk)\n lastChunk = chunk\n } else {\n if (canMergeBlocks(lastChunk, chunk)) {\n if (chunk.maxv.compareTo(lastChunk.maxv) > 0) {\n lastChunk.maxv = chunk.maxv\n }\n } else {\n mergedChunks.push(chunk)\n lastChunk = chunk\n }\n }\n }\n })\n\n return mergedChunks\n}\n","import { Buffer } from 'buffer'\nexport default class VirtualOffset {\n public blockPosition: number\n public dataPosition: number\n constructor(blockPosition: number, dataPosition: number) {\n this.blockPosition = blockPosition // < offset of the compressed data block\n this.dataPosition = dataPosition // < offset into the uncompressed data\n }\n\n toString() {\n return `${this.blockPosition}:${this.dataPosition}`\n }\n\n compareTo(b: VirtualOffset) {\n return (\n this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition\n )\n }\n}\nexport function fromBytes(bytes: Buffer, offset = 0, bigendian = false) {\n if (bigendian) {\n throw new Error('big-endian virtual file offsets not implemented')\n }\n\n return new VirtualOffset(\n bytes[offset + 7]! * 0x10000000000 +\n bytes[offset + 6]! * 0x100000000 +\n bytes[offset + 5]! * 0x1000000 +\n bytes[offset + 4]! * 0x10000 +\n bytes[offset + 3]! * 0x100 +\n bytes[offset + 2]!,\n (bytes[offset + 1]! << 8) | bytes[offset]!,\n )\n}\n","import VirtualOffset from './virtualOffset'\n\n// little class representing a chunk in the index\nexport default class Chunk {\n public minv: VirtualOffset\n public maxv: VirtualOffset\n public bin: number\n public _fetchedSize?: number\n\n constructor(\n minv: VirtualOffset,\n maxv: VirtualOffset,\n bin: number,\n fetchedSize = undefined,\n ) {\n this.minv = minv\n this.maxv = maxv\n this.bin = bin\n this._fetchedSize = fetchedSize\n }\n\n toUniqueString() {\n \n return `${this.minv}..${this.maxv} (bin ${\n this.bin\n }, fetchedSize ${this.fetchedSize()})`\n }\n\n toString() {\n return this.toUniqueString()\n }\n\n compareTo(b: Chunk) {\n return (\n this.minv.compareTo(b.minv) ||\n this.maxv.compareTo(b.maxv) ||\n this.bin - b.bin\n )\n }\n\n fetchedSize() {\n if (this._fetchedSize !== undefined) {\n return this._fetchedSize\n }\n return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition\n }\n}\n","import { GenericFilehandle } from 'generic-filehandle'\nimport VirtualOffset from './virtualOffset'\nimport Chunk from './chunk'\n\nexport interface Options {\n // support having some unknown parts of the options\n [key: string]: unknown\n signal?: AbortSignal\n}\n\nexport interface IndexData {\n refNameToId: Record<string, number>\n refIdToName: string[]\n metaChar: string | null\n columnNumbers: { ref: number; start: number; end: number }\n coordinateType: string\n format: string\n [key: string]: any\n}\n\nexport default abstract class IndexFile {\n public filehandle: GenericFilehandle\n public renameRefSeq: (arg0: string) => string\n private parseP?: Promise<IndexData>\n\n constructor({\n filehandle,\n renameRefSeqs = (n: string) => n,\n }: {\n filehandle: GenericFilehandle\n renameRefSeqs?: (a: string) => string\n }) {\n this.filehandle = filehandle\n this.renameRefSeq = renameRefSeqs\n }\n\n public abstract lineCount(refName: string, args: Options): Promise<number>\n\n protected abstract _parse(opts: Options): Promise<IndexData>\n\n public async getMetadata(opts: Options = {}) {\n const { indices: _indices, ...rest } = await this.parse(opts)\n return rest\n }\n\n public abstract blocksForRange(\n refName: string,\n start: number,\n end: number,\n opts: Options,\n ): Promise<Chunk[]>\n\n _findFirstData(\n currentFdl: VirtualOffset | undefined,\n virtualOffset: VirtualOffset,\n ) {\n if (currentFdl) {\n return currentFdl.compareTo(virtualOffset) > 0\n ? virtualOffset\n : currentFdl\n } else {\n return virtualOffset\n }\n }\n\n async parse(opts: Options = {}) {\n if (!this.parseP) {\n this.parseP = this._parse(opts).catch((e: unknown) => {\n this.parseP = undefined\n throw e\n })\n }\n return this.parseP\n }\n\n async hasRefSeq(seqId: number, opts: Options = {}) {\n const idx = await this.parse(opts)\n return !!idx.indices[seqId]?.binIndex\n }\n}\n","import Long from 'long'\nimport { Buffer } from 'buffer'\nimport VirtualOffset, { fromBytes } from './virtualOffset'\nimport Chunk from './chunk'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { longToNumber, optimizeChunks, checkAbortSignal } from './util'\nimport IndexFile, { Options } from './indexFile'\n\nconst TBI_MAGIC = 21578324 // TBI\\1\nconst TAD_LIDX_SHIFT = 14\n\n/**\n * calculate the list of bins that may overlap with region [beg,end)\n * (zero-based half-open)\n */\nfunction reg2bins(beg: number, end: number) {\n beg += 1 // < convert to 1-based closed\n end -= 1\n return [\n [0, 0],\n [1 + (beg >> 26), 1 + (end >> 26)],\n [9 + (beg >> 23), 9 + (end >> 23)],\n [73 + (beg >> 20), 73 + (end >> 20)],\n [585 + (beg >> 17), 585 + (end >> 17)],\n [4681 + (beg >> 14), 4681 + (end >> 14)],\n ] as const\n}\n\nexport default class TabixIndex extends IndexFile {\n async lineCount(refName: string, opts: Options = {}) {\n const indexData = await this.parse(opts)\n const refId = indexData.refNameToId[refName]\n if (refId === undefined) {\n return -1\n }\n const idx = indexData.indices[refId]\n if (!idx) {\n return -1\n }\n const { stats } = indexData.indices[refId]\n if (stats) {\n return stats.lineCount\n }\n return -1\n }\n\n // fetch and parse the index\n async _parse(opts: Options = {}) {\n const buf = await this.filehandle.readFile(opts)\n const bytes = await unzip(buf)\n checkAbortSignal(opts.signal)\n\n // check TBI magic numbers\n if (bytes.readUInt32LE(0) !== TBI_MAGIC /* \"TBI\\1\" */) {\n throw new Error('Not a TBI file')\n // TODO: do we need to support big-endian TBI files?\n }\n\n // number of reference sequences in the index\n const refCount = bytes.readInt32LE(4)\n const formatFlags = bytes.readInt32LE(8)\n const coordinateType =\n formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'\n const formatOpts: Record<number, string> = {\n 0: 'generic',\n 1: 'SAM',\n 2: 'VCF',\n }\n const format = formatOpts[formatFlags & 0xf]\n if (!format) {\n throw new Error(`invalid Tabix preset format flags ${formatFlags}`)\n }\n const columnNumbers = {\n ref: bytes.readInt32LE(12),\n start: bytes.readInt32LE(16),\n end: bytes.readInt32LE(20),\n }\n const metaValue = bytes.readInt32LE(24)\n const depth = 5\n const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7\n const maxRefLength = 2 ** (14 + depth * 3)\n const metaChar = metaValue ? String.fromCharCode(metaValue) : null\n const skipLines = bytes.readInt32LE(28)\n\n // read sequence dictionary\n const nameSectionLength = bytes.readInt32LE(32)\n const { refNameToId, refIdToName } = this._parseNameBytes(\n bytes.slice(36, 36 + nameSectionLength),\n )\n\n // read the indexes for each reference sequence\n let currOffset = 36 + nameSectionLength\n let firstDataLine: VirtualOffset | undefined\n const indices = new Array(refCount).fill(0).map(() => {\n // the binning index\n const binCount = bytes.readInt32LE(currOffset)\n currOffset += 4\n const binIndex: Record<number, Chunk[]> = {}\n let stats\n for (let j = 0; j < binCount; j += 1) {\n const bin = bytes.readUInt32LE(currOffset)\n currOffset += 4\n if (bin > maxBinNumber + 1) {\n throw new Error(\n 'tabix index contains too many bins, please use a CSI index',\n )\n } else if (bin === maxBinNumber + 1) {\n const chunkCount = bytes.readInt32LE(currOffset)\n currOffset += 4\n if (chunkCount === 2) {\n stats = this.parsePseudoBin(bytes, currOffset)\n }\n currOffset += 16 * chunkCount\n } else {\n const chunkCount = bytes.readInt32LE(currOffset)\n currOffset += 4\n const chunks = new Array(chunkCount)\n for (let k = 0; k < chunkCount; k += 1) {\n const u = fromBytes(bytes, currOffset)\n const v = fromBytes(bytes, currOffset + 8)\n currOffset += 16\n firstDataLine = this._findFirstData(firstDataLine, u)\n chunks[k] = new Chunk(u, v, bin)\n }\n binIndex[bin] = chunks\n }\n }\n\n // the linear index\n const linearCount = bytes.readInt32LE(currOffset)\n currOffset += 4\n const linearIndex = new Array(linearCount)\n for (let k = 0; k < linearCount; k += 1) {\n linearIndex[k] = fromBytes(bytes, currOffset)\n currOffset += 8\n firstDataLine = this._findFirstData(firstDataLine, linearIndex[k])\n }\n return { binIndex, linearIndex, stats }\n })\n\n return {\n indices,\n metaChar,\n maxBinNumber,\n maxRefLength,\n skipLines,\n firstDataLine,\n columnNumbers,\n coordinateType,\n format,\n refIdToName,\n refNameToId,\n maxBlockSize: 1 << 16,\n }\n }\n\n parsePseudoBin(bytes: Buffer, offset: number) {\n const lineCount = longToNumber(\n Long.fromBytesLE(\n bytes.slice(offset + 16, offset + 24) as unknown as number[],\n true,\n ),\n )\n return { lineCount }\n }\n\n _parseNameBytes(namesBytes: Buffer) {\n let currRefId = 0\n let currNameStart = 0\n const refIdToName: string[] = []\n const refNameToId: Record<string, number> = {}\n for (let i = 0; i < namesBytes.length; i += 1) {\n if (!namesBytes[i]) {\n if (currNameStart < i) {\n let refName = namesBytes.toString('utf8', currNameStart, i)\n refName = this.renameRefSeq(refName)\n refIdToName[currRefId] = refName\n refNameToId[refName] = currRefId\n }\n currNameStart = i + 1\n currRefId += 1\n }\n }\n return { refNameToId, refIdToName }\n }\n\n async blocksForRange(\n refName: string,\n min: number,\n max: number,\n opts: Options = {},\n ) {\n if (min < 0) {\n min = 0\n }\n\n const indexData = await this.parse(opts)\n const refId = indexData.refNameToId[refName]\n if (refId === undefined) {\n return []\n }\n const ba = indexData.indices[refId]\n if (!ba) {\n return []\n }\n\n const minOffset = ba.linearIndex.length\n ? ba.linearIndex[\n min >> TAD_LIDX_SHIFT >= ba.linearIndex.length\n ? ba.linearIndex.length - 1\n : min >> TAD_LIDX_SHIFT\n ]\n : new VirtualOffset(0, 0)\n if (!minOffset) {\n console.warn('querying outside of possible tabix range')\n }\n\n // const { linearIndex, binIndex } = indexes\n\n const overlappingBins = reg2bins(min, max) // List of bin #s that overlap min, max\n const chunks: Chunk[] = []\n\n // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned\n for (const [start, end] of overlappingBins) {\n for (let bin = start; bin <= end; bin++) {\n if (ba.binIndex[bin]) {\n for (const c of ba.binIndex[bin]) {\n chunks.push(new Chunk(c.minv, c.maxv, bin))\n }\n }\n }\n }\n\n // Use the linear index to find minimum file position of chunks that could\n // contain alignments in the region\n const nintv = ba.linearIndex.length\n let lowest = null\n const minLin = Math.min(min >> 14, nintv - 1)\n const maxLin = Math.min(max >> 14, nintv - 1)\n for (let i = minLin; i <= maxLin; ++i) {\n const vp = ba.linearIndex[i]\n if (vp) {\n if (!lowest || vp.compareTo(lowest) < 0) {\n lowest = vp\n }\n }\n }\n\n return optimizeChunks(chunks, lowest)\n }\n}\n","import Long from 'long'\nimport { Buffer } from 'buffer'\nimport { unzip } from '@gmod/bgzf-filehandle'\n\nimport VirtualOffset, { fromBytes } from './virtualOffset'\nimport Chunk from './chunk'\nimport { longToNumber, optimizeChunks } from './util'\n\nimport IndexFile, { Options } from './indexFile'\n\nconst CSI1_MAGIC = 21582659 // CSI\\1\nconst CSI2_MAGIC = 38359875 // CSI\\2\n\nfunction lshift(num: number, bits: number) {\n return num * 2 ** bits\n}\nfunction rshift(num: number, bits: number) {\n return Math.floor(num / 2 ** bits)\n}\n\nexport default class CSI extends IndexFile {\n private maxBinNumber: number\n private depth: number\n private minShift: number\n constructor(args: any) {\n super(args)\n this.maxBinNumber = 0\n this.depth = 0\n this.minShift = 0\n }\n async lineCount(refName: string, opts: Options = {}): Promise<number> {\n const indexData = await this.parse(opts)\n const refId = indexData.refNameToId[refName]\n if (refId === undefined) {\n return -1\n }\n const idx = indexData.indices[refId]\n if (!idx) {\n return -1\n }\n const { stats } = indexData.indices[refId]\n if (stats) {\n return stats.lineCount\n }\n return -1\n }\n\n indexCov() {\n throw new Error('CSI indexes do not support indexcov')\n }\n\n parseAuxData(bytes: Buffer, offset: number) {\n const formatFlags = bytes.readInt32LE(offset)\n const coordinateType =\n formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'\n const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf]\n if (!format) {\n throw new Error(`invalid Tabix preset format flags ${formatFlags}`)\n }\n const columnNumbers = {\n ref: bytes.readInt32LE(offset + 4),\n start: bytes.readInt32LE(offset + 8),\n end: bytes.readInt32LE(offset + 12),\n }\n const metaValue = bytes.readInt32LE(offset + 16)\n const metaChar = metaValue ? String.fromCharCode(metaValue) : null\n const skipLines = bytes.readInt32LE(offset + 20)\n const nameSectionLength = bytes.readInt32LE(offset + 24)\n\n const { refIdToName, refNameToId } = this._parseNameBytes(\n bytes.slice(offset + 28, offset + 28 + nameSectionLength),\n )\n\n return {\n refIdToName,\n refNameToId,\n skipLines,\n metaChar,\n columnNumbers,\n format,\n coordinateType,\n }\n }\n\n _parseNameBytes(namesBytes: Buffer) {\n let currRefId = 0\n let currNameStart = 0\n const refIdToName = []\n const refNameToId: Record<string, number> = {}\n for (let i = 0; i < namesBytes.length; i += 1) {\n if (!namesBytes[i]) {\n if (currNameStart < i) {\n let refName = namesBytes.toString('utf8', currNameStart, i)\n refName = this.renameRefSeq(refName)\n refIdToName[currRefId] = refName\n refNameToId[refName] = currRefId\n }\n currNameStart = i + 1\n currRefId += 1\n }\n }\n return { refNameToId, refIdToName }\n }\n\n // fetch and parse the index\n\n async _parse(opts: Options = {}) {\n const bytes = await unzip(await this.filehandle.readFile(opts))\n\n // check TBI magic numbers\n let csiVersion\n if (bytes.readUInt32LE(0) === CSI1_MAGIC) {\n csiVersion = 1\n } else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {\n csiVersion = 2\n } else {\n throw new Error('Not a CSI file')\n // TODO: do we need to support big-endian CSI files?\n }\n\n this.minShift = bytes.readInt32LE(4)\n this.depth = bytes.readInt32LE(8)\n this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7\n const maxRefLength = 2 ** (this.minShift + this.depth * 3)\n const auxLength = bytes.readInt32LE(12)\n const aux =\n auxLength && auxLength >= 30\n ? this.parseAuxData(bytes, 16)\n : {\n refIdToName: [],\n refNameToId: {},\n metaChar: null,\n columnNumbers: { ref: 0, start: 1, end: 2 },\n coordinateType: 'zero-based-half-open',\n format: 'generic',\n }\n const refCount = bytes.readInt32LE(16 + auxLength)\n\n // read the indexes for each reference sequence\n let firstDataLine: VirtualOffset | undefined\n let currOffset = 16 + auxLength + 4\n const indices = new Array(refCount).fill(0).map(() => {\n // the binning index\n const binCount = bytes.readInt32LE(currOffset)\n currOffset += 4\n const binIndex: Record<string, Chunk[]> = {}\n let stats // < provided by parsing a pseudo-bin, if present\n for (let j = 0; j < binCount; j += 1) {\n const bin = bytes.readUInt32LE(currOffset)\n if (bin > this.maxBinNumber) {\n // this is a fake bin that actually has stats information\n // about the reference sequence in it\n stats = this.parsePseudoBin(bytes, currOffset + 4)\n currOffset += 4 + 8 + 4 + 16 + 16\n } else {\n const loffset = fromBytes(bytes, currOffset + 4)\n firstDataLine = this._findFirstData(firstDataLine, loffset)\n const chunkCount = bytes.readInt32LE(currOffset + 12)\n currOffset += 16\n const chunks = new Array(chunkCount)\n for (let k = 0; k < chunkCount; k += 1) {\n const u = fromBytes(bytes, currOffset)\n const v = fromBytes(bytes, currOffset + 8)\n currOffset += 16\n // this._findFirstData(data, u)\n chunks[k] = new Chunk(u, v, bin)\n }\n binIndex[bin] = chunks\n }\n }\n\n return { binIndex, stats }\n })\n\n return {\n ...aux,\n csi: true,\n refCount,\n maxBlockSize: 1 << 16,\n firstDataLine,\n csiVersion,\n indices,\n depth: this.depth,\n maxBinNumber: this.maxBinNumber,\n maxRefLength,\n }\n }\n\n parsePseudoBin(bytes: Buffer, offset: number) {\n const lineCount = longToNumber(\n Long.fromBytesLE(\n bytes.slice(offset + 28, offset + 36) as unknown as number[],\n true,\n ),\n )\n return { lineCount }\n }\n\n async blocksForRange(\n refName: string,\n min: number,\n max: number,\n opts: Options = {},\n ) {\n if (min < 0) {\n min = 0\n }\n\n const indexData = await this.parse(opts)\n const refId = indexData.refNameToId[refName]\n if (refId === undefined) {\n return []\n }\n const ba = indexData.indices[refId]\n if (!ba) {\n return []\n }\n\n // const { linearIndex, binIndex } = indexes\n\n const overlappingBins = this.reg2bins(min, max) // List of bin #s that overlap min, max\n const chunks: Chunk[] = []\n\n // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned\n for (const [start, end] of overlappingBins) {\n for (let bin = start; bin <= end; bin++) {\n if (ba.binIndex[bin]) {\n for (const c of ba.binIndex[bin]) {\n chunks.push(new Chunk(c.minv, c.maxv, bin))\n }\n }\n }\n }\n\n return optimizeChunks(chunks, new VirtualOffset(0, 0))\n }\n\n /**\n * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)\n */\n reg2bins(beg: number, end: number) {\n beg -= 1 // < convert to 1-based closed\n if (beg < 1) {\n beg = 1\n }\n if (end > 2 ** 50) {\n end = 2 ** 34\n } // 17 GiB ought to be enough for anybody\n end -= 1\n let l = 0\n let t = 0\n let s = this.minShift + this.depth * 3\n const bins = []\n for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {\n const b = t + rshift(beg, s)\n const e = t + rshift(end, s)\n if (e - b + bins.length > this.maxBinNumber) {\n throw new Error(\n `query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`,\n )\n }\n bins.push([b, e] as const)\n }\n return bins\n }\n}\n","import AbortablePromiseCache from '@gmod/abortable-promise-cache'\nimport LRU from 'quick-lru'\nimport { Buffer } from 'buffer'\nimport { GenericFilehandle, RemoteFile, LocalFile } from 'generic-filehandle'\nimport { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'\nimport { checkAbortSignal } from './util'\nimport IndexFile, { Options, IndexData } from './indexFile'\n\nimport Chunk from './chunk'\nimport TBI from './tbi'\nimport CSI from './csi'\n\ntype GetLinesCallback = (line: string, fileOffset: number) => void\n\nconst decoder =\n typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined\n\ninterface GetLinesOpts {\n [key: string]: unknown\n signal?: AbortSignal\n lineCallback: GetLinesCallback\n}\n\ninterface ReadChunk {\n buffer: Buffer\n cpositions: number[]\n dpositions: number[]\n}\n\nfunction timeout(time: number) {\n return new Promise(resolve => setTimeout(resolve, time))\n}\nexport default class TabixIndexedFile {\n private filehandle: GenericFilehandle\n private index: IndexFile\n private yieldTime: number\n private renameRefSeq: (n: string) => string\n private chunkCache: AbortablePromiseCache<Chunk, ReadChunk>\n\n /**\n * @param {object} args\n *\n * @param {string} [args.path]\n *\n * @param {filehandle} [args.filehandle]\n *\n * @param {string} [args.tbiPath]\n *\n * @param {filehandle} [args.tbiFilehandle]\n *\n * @param {string} [args.csiPath]\n *\n * @param {filehandle} [args.csiFilehandle]\n *\n * @param {number} [args.yieldTime] yield to main thread after N milliseconds\n * if reading features is taking a long time to avoid hanging main thread\n *\n * @param {function} [args.renameRefSeqs] optional function with sig `string\n * => string` to transform reference sequence names for the purpose of\n * indexing and querying. note that the data that is returned is not altered,\n * just the names of the reference sequences that are used for querying.\n */\n constructor({\n path,\n filehandle,\n url,\n tbiPath,\n tbiUrl,\n tbiFilehandle,\n csiPath,\n csiUrl,\n csiFilehandle,\n yieldTime = 500,\n renameRefSeqs = n => n,\n chunkCacheSize = 5 * 2 ** 20,\n }: {\n path?: string\n filehandle?: GenericFilehandle\n url?: string\n tbiPath?: string\n tbiUrl?: string\n tbiFilehandle?: GenericFilehandle\n csiPath?: string\n csiUrl?: string\n csiFilehandle?: GenericFilehandle\n yieldTime?: number\n renameRefSeqs?: (n: string) => string\n chunkCacheSize?: number\n }) {\n if (filehandle) {\n this.filehandle = filehandle\n } else if (path) {\n this.filehandle = new LocalFile(path)\n } else if (url) {\n this.filehandle = new RemoteFile(url)\n } else {\n throw new TypeError('must provide either filehandle or path')\n }\n\n if (tbiFilehandle) {\n this.index = new TBI({\n filehandle: tbiFilehandle,\n renameRefSeqs,\n })\n } else if (csiFilehandle) {\n this.index = new CSI({\n filehandle: csiFilehandle,\n renameRefSeqs,\n })\n } else if (tbiPath) {\n this.index = new TBI({\n filehandle: new LocalFile(tbiPath),\n renameRefSeqs,\n })\n } else if (csiPath) {\n this.index = new CSI({\n filehandle: new LocalFile(csiPath),\n renameRefSeqs,\n })\n } else if (path) {\n this.index = new TBI({\n filehandle: new LocalFile(`${path}.tbi`),\n renameRefSeqs,\n })\n } else if (csiUrl) {\n this.index = new CSI({\n filehandle: new RemoteFile(csiUrl),\n })\n } else if (tbiUrl) {\n this.index = new TBI({\n filehandle: new RemoteFile(tbiUrl),\n })\n } else if (url) {\n this.index = new TBI({\n filehandle: new RemoteFile(`${url}.tbi`),\n })\n } else {\n throw new TypeError(\n 'must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl',\n )\n }\n\n this.renameRefSeq = renameRefSeqs\n this.yieldTime = yieldTime\n this.chunkCache = new AbortablePromiseCache<Chunk, ReadChunk>({\n cache: new LRU({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),\n fill: (args: Chunk, signal?: AbortSignal) =>\n this.readChunk(args, { signal }),\n })\n }\n\n /**\n * @param refName name of the reference sequence\n *\n * @param start start of the region (in 0-based half-open coordinates)\n *\n * @param end end of the region (in 0-based half-open coordinates)\n *\n * @param opts callback called for each line in the region. can also pass a\n * object param containing obj.lineCallback, obj.signal, etc\n *\n * @returns promise that is resolved when the whole read is finished,\n * rejected on error\n */\n async getLines(\n refName: string,\n s: number | undefined,\n e: number | undefined,\n opts: GetLinesOpts | GetLinesCallback,\n ) {\n let signal: AbortSignal | undefined\n let options: Options = {}\n let callback: (line: string, lineOffset: number) => void\n\n if (typeof opts === 'function') {\n callback = opts\n } else {\n options = opts\n callback = opts.lineCallback\n signal = opts.signal\n }\n\n const metadata = await this.index.getMetadata(options)\n checkAbortSignal(signal)\n const start = s ?? 0\n const end = e ?? metadata.maxRefLength\n if (!(start <= end)) {\n throw new TypeError(\n 'invalid start and end coordinates. start must be less than or equal to end',\n )\n }\n if (start === end) {\n return\n }\n\n const chunks = await this.index.blocksForRange(refName, start, end, options)\n checkAbortSignal(signal)\n\n // now go through each chunk and parse and filter the lines out of it\n let last = Date.now()\n for (const c of chunks) {\n let previousStartCoordinate: number | undefined\n const { buffer, cpositions, dpositions } = await this.chunkCache.get(\n c.toString(),\n c,\n signal,\n )\n\n checkAbortSignal(signal)\n let blockStart = 0\n let pos = 0\n while (blockStart < buffer.length) {\n const n = buffer.indexOf('\\n', blockStart)\n if (n === -1) {\n break\n }\n const b = buffer.slice(blockStart, n)\n const line = decoder?.decode(b) ?? b.toString()\n\n // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n if (dpositions) {\n while (blockStart + c.minv.dataPosition >= dpositions[pos++]!) {}\n pos--\n }\n\n // filter the line for whether it is within the requested range\n const { startCoordinate, overlaps } = this.checkLine(\n metadata,\n refName,\n start,\n end,\n line,\n )\n\n // do a small check just to make sure that the lines are really sorted\n // by start coordinate\n if (\n previousStartCoordinate !== undefined &&\n startCoordinate !== undefined &&\n previousStartCoordinate > startCoordinate\n ) {\n throw new Error(\n `Lines not sorted by start coordinate (${previousStartCoordinate} > ${startCoordinate}), this file is not usable with Tabix.`,\n )\n }\n previousStartCoordinate = startCoordinate\n\n if (overlaps) {\n callback(\n line.trim(),\n // cpositions[pos] refers to actual file offset of a bgzip block boundaries\n //\n // we multiply by (1 <<8) in order to make sure each block has a \"unique\"\n // address space so that data in that block could never overlap\n //\n // then the blockStart-dpositions is an uncompressed file offset from\n // that bgzip block boundary, and since the cpositions are multiplied by\n // (1 << 8) these uncompressed offsets get a unique space\n cpositions[pos]! * (1 << 8) +\n (blockStart - dpositions[pos]!) +\n c.minv.dataPosition +\n 1,\n )\n } else if (startCoordinate !== undefined && startCoordinate >= end) {\n // the lines were overlapping the region, but now have stopped, so\n // we must be at the end of the relevant data and we can stop\n // processing data now\n return\n }\n\n // yield if we have emitted beyond the yield limit\n if (this.yieldTime && last - Date.now() > this.yieldTime) {\n last = Date.now()\n checkAbortSignal(signal)\n await timeout(1)\n }\n blockStart = n + 1\n }\n }\n }\n\n async getMetadata(opts: Options = {}) {\n return this.index.getMetadata(opts)\n }\n\n /**\n * get a buffer containing the \"header\" region of the file, which are the\n * bytes up to the first non-meta line\n */\n async getHeaderBuffer(opts: Options = {}) {\n const { firstDataLine, metaChar, maxBlockSize } =\n await this.getMetadata(opts)\n checkAbortSignal(opts.signal)\n\n // eslint-disable-next-line @typescript-eslint/restrict-plus-operands\n const maxFetch = (firstDataLine?.blockPosition || 0) + maxBlockSize\n // TODO: what if we don't have a firstDataLine, and the header\n // actually takes up more than one block? this case is not covered here\n\n const buf = await this._readRegion(0, maxFetch, opts)\n const bytes = await unzip(buf)\n\n // trim off lines after the last non-meta line\n if (metaChar) {\n // trim backward from the end\n let lastNewline = -1\n const newlineByte = '\\n'.charCodeAt(0)\n const metaByte = metaChar.charCodeAt(0)\n for (let i = 0; i < bytes.length; i += 1) {\n if (i === lastNewline + 1 && bytes[i] !== metaByte) {\n break\n }\n if (bytes[i] === newlineByte) {\n lastNewline = i\n }\n }\n return bytes.slice(0, lastNewline + 1)\n }\n return bytes\n }\n\n /**\n * get a string containing the \"header\" region of the file, is the portion up\n * to the first non-meta line\n *\n * @returns {Promise} for a string\n */\n async getHeader(opts: Options = {}) {\n const bytes = await this.getHeaderBuffer(opts)\n return bytes.toString('utf8')\n }\n\n /**\n * get an array of reference sequence names, in the order in which they occur\n * in the file. reference sequence renaming is not applied to these names.\n */\n async getReferenceSequenceNames(opts: Options = {}) {\n const metadata = await this.getMetadata(opts)\n return metadata.refIdToName\n }\n\n /**\n * @param {object} metadata metadata object from the parsed index, containing\n * columnNumbers, metaChar, and format\n *\n * @param {string} regionRefName\n *\n * @param {number} regionStart region start coordinate (0-based-half-open)\n *\n * @param {number} regionEnd region end coordinate (0-based-half-open)\n *\n * @param {array[string]} line\n *\n * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,\n * true if line is a data line that overlaps the given region\n */\n checkLine(\n metadata: IndexData,\n regionRefName: string,\n regionStart: number,\n regionEnd: number,\n line: string,\n ) {\n const { columnNumbers, metaChar, coordinateType, format } = metadata\n // skip meta lines\n if (metaChar && line.startsWith(metaChar)) {\n return { overlaps: false }\n }\n\n // check ref/start/end using column metadata from index\n let { ref, start, end } = columnNumbers\n if (!ref) {\n ref = 0\n }\n if (!start) {\n start = 0\n }\n if (!end) {\n end = 0\n }\n if (format === 'VCF') {\n end = 8\n }\n const maxColumn = Math.max(ref, start, end)\n\n // this code is kind of complex, but it is fairly fast. basically, we want\n // to avoid doing a split, because if the lines are really long that could\n // lead to us allocating a bunch of extra memory, which is slow\n\n let currentColumnNumber = 1 // cols are numbered starting at 1 in the index metadata\n let currentColumnStart = 0\n let refSeq = ''\n let startCoordinate = -Infinity\n for (let i = 0; i < line.length + 1; i += 1) {\n if (line[i] === '\\t' || i === line.length) {\n if (currentColumnNumber === ref) {\n if (\n this.renameRefSeq(line.slice(currentColumnStart, i)) !==\n regionRefName\n ) {\n return { overlaps: false }\n }\n } else if (currentColumnNumber === start) {\n startCoordinate = parseInt(line.slice(currentColumnStart, i), 10)\n // we convert to 0-based-half-open\n if (coordinateType === '1-based-closed') {\n startCoordinate -= 1\n }\n if (startCoordinate >= regionEnd) {\n return { startCoordinate, overlaps: false }\n }\n if (end === 0 || end === start) {\n // if we have no end, we assume the feature is 1 bp long\n if (startCoordinate + 1 <= regionStart) {\n return { startCoordinate, overlaps: false }\n }\n }\n } else if (format === 'VCF' && currentColumnNumber === 4) {\n refSeq = line.slice(currentColumnStart, i)\n } else if (currentColumnNumber === end) {\n // this will never match if there is no end column\n const endCoordinate =\n format === 'VCF'\n ? this._getVcfEnd(\n startCoordinate,\n refSeq,\n line.slice(currentColumnStart, i),\n )\n : parseInt(line.slice(currentColumnStart, i), 10)\n if (endCoordinate <= regionStart) {\n return { overlaps: false }\n }\n }\n currentColumnStart = i + 1\n currentColumnNumber += 1\n if (currentColumnNumber > maxColumn) {\n break\n }\n }\n }\n return { startCoordinate, overlaps: true }\n }\n\n _getVcfEnd(startCoordinate: number, refSeq: string, info: any) {\n let endCoordinate = startCoordinate + refSeq.length\n // ignore TRA features as they specify CHR2 and END as being on a different\n // chromosome\n //\n // if CHR2 is on the same chromosome, still ignore it because there should\n // be another pairwise feature at the end of this one\n const isTRA = info.includes('SVTYPE=TRA')\n if (info[0] !== '.' && !isTRA) {\n let prevChar = ';'\n for (let j = 0; j < info.length; j += 1) {\n if (prevChar === ';' && info.slice(j, j + 4) === 'END=') {\n let valueEnd = info.indexOf(';', j)\n if (valueEnd === -1) {\n valueEnd = info.length\n }\n endCoordinate = parseInt(info.slice(j + 4, valueEnd), 10)\n break\n }\n prevChar = info[j]\n }\n } else if (isTRA) {\n return startCoordinate + 1\n }\n return endCoordinate\n }\n\n /**\n * return the approximate number of data lines in the given reference\n * sequence\n *\n * @param refSeq reference sequence name\n *\n * @returns number of data lines present on that reference sequence\n */\n async lineCount(refName: string, opts: Options = {}) {\n return this.index.lineCount(refName, opts)\n }\n\n async _readRegion(pos: number, size: number, opts: Options = {}) {\n const b = Buffer.alloc(size)\n const { bytesRead, buffer } = await this.filehandle.read(\n b,\n 0,\n size,\n pos,\n opts,\n )\n\n return buffer.slice(0, bytesRead)\n }\n\n /**\n * read and uncompress the data in a chunk (composed of one or more\n * contiguous bgzip blocks) of the file\n */\n async readChunk(c: Chunk, opts: Options = {}) {\n // fetch the uncompressed data, uncompress carefully a block at a time, and\n // stop when done\n\n const data = await this._readRegion(\n c.minv.blockPosition,\n c.fetchedSize(),\n opts,\n )\n return unzipChunkSlice(data, c)\n 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