jbrowse2: x/static/js/4499.3f0b2e70.chunk.js.map comparison

comparison x/static/js/4499.3f0b2e70.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

comparison

equal deleted inserted replaced

124:137e08517410	125:49f3d3878413
	1 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{ 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","/*\n Created by Alex Bol on 4/1/2017.\n /\n\n/\n Interval is a pair of numbers or a pair of any comparable objects on which may be defined predicates\n * equal, less and method max(p1, p1) that returns maximum in a pair.\n * When interval is an object rather than a pair of numbers, this object should have properties low, high, max\n * and implement methods less_than(), equal_to(), intersect(), not_intersect(), clone(), output().\n * Two static methods comparable_max(), comparable_less_than() define how to compare values in pair. <br/>\n * This interface is described in typescript definition file index.d.ts\n \n Axis aligned rectangle is an example of such interval.\n * We may look at rectangle as an interval between its low left and top right corners.\n * See Box class in [flatten-js](https://github.com/alexbol99/flatten-js) library as the example\n * of Interval interface implementation\n * @type {Interval}\n /\nconst Interval = class Interval {\n /\n Accept two comparable values and creates new instance of interval\n * Predicate Interval.comparable_less(low, high) supposed to return true on these values\n * @param low\n * @param high\n /\n constructor(low, high) {\n this.low = low;\n this.high = high;\n }\n\n /\n Clone interval\n * @returns {Interval}\n /\n clone() {\n return new Interval(this.low, this.high);\n }\n\n /\n Propery max returns clone of this interval\n * @returns {Interval}\n /\n get max() {\n return this.clone(); // this.high;\n }\n\n /\n Predicate returns true is this interval less than other interval\n * @param other_interval\n * @returns {boolean}\n /\n less_than(other_interval) {\n return this.low < other_interval.low \|\|\n this.low === other_interval.low && this.high < other_interval.high;\n }\n\n /\n Predicate returns true is this interval equals to other interval\n * @param other_interval\n * @returns {boolean}\n /\n equal_to(other_interval) {\n return this.low === other_interval.low && this.high === other_interval.high;\n }\n\n /\n Predicate returns true if this interval intersects other interval\n * @param other_interval\n * @returns {boolean}\n /\n intersect(other_interval) {\n return !this.not_intersect(other_interval);\n }\n\n /\n Predicate returns true if this interval does not intersect other interval\n * @param other_interval\n * @returns {boolean}\n /\n not_intersect(other_interval) {\n return (this.high < other_interval.low \|\| other_interval.high < this.low);\n }\n\n /\n Returns new interval merged with other interval\n * @param {Interval} other_interval - Other interval to merge with\n * @returns {Interval}\n /\n merge(other_interval) {\n return new Interval(\n this.low === undefined ?\n other_interval.low : (this.low < other_interval.low ? this.low : other_interval.low),\n this.high === undefined ?\n other_interval.high : (this.high > other_interval.high ? this.high : other_interval.high)\n );\n }\n\n /\n Returns how key should return\n /\n output() {\n return [this.low, this.high];\n }\n\n /\n Function returns maximum between two comparable values\n * @param interval1\n * @param interval2\n * @returns {Interval}\n /\n static comparable_max(interval1, interval2) {\n return interval1.merge(interval2);\n }\n\n /\n Predicate returns true if first value less than second value\n * @param val1\n * @param val2\n * @returns {boolean}\n /\n static comparable_less_than(val1, val2 ) {\n return val1 < val2;\n }\n};\n\n/\n Created by Alex Bol on 3/28/2017.\n /\n\n\n// module.exports = {\n// RB_TREE_COLOR_RED: 0,\n// RB_TREE_COLOR_BLACK: 1\n// };\n\nconst RB_TREE_COLOR_RED = 0;\nconst RB_TREE_COLOR_BLACK = 1;\n\n/\n Created by Alex Bol on 4/1/2017.\n /\n\n\nclass Node {\n constructor(key = undefined, value = undefined,\n left = null, right = null, parent = null, color = RB_TREE_COLOR_BLACK) {\n this.left = left; // reference to left child node\n this.right = right; // reference to right child node\n this.parent = parent; // reference to parent node\n this.color = color;\n\n this.item = {key: key, value: value}; // key is supposed to be instance of Interval\n\n / If not, this should by an array of two numbers /\n if (key && key instanceof Array && key.length === 2) {\n if (!Number.isNaN(key[0]) && !Number.isNaN(key[1])) {\n let [low, high] = key;\n if (low > high) [low, high] = [high, low];\n this.item.key = new Interval(low, high);\n }\n }\n\n this.max = this.item.key ? this.item.key.max : undefined;\n }\n\n isNil() {\n return (this.item.key === undefined && this.item.value === undefined &&\n this.left === null && this.right === null && this.color === RB_TREE_COLOR_BLACK);\n }\n\n _value_less_than(other_node) {\n return this.item.value && other_node.item.value && this.item.value.less_than ?\n this.item.value.less_than(other_node.item.value) :\n this.item.value < other_node.item.value;\n }\n\n less_than(other_node) {\n // if tree stores only keys\n if (this.item.value === this.item.key && other_node.item.value === other_node.item.key) {\n return this.item.key.less_than(other_node.item.key);\n }\n else { // if tree stores keys and values\n return this.item.key.less_than(other_node.item.key) \|\|\n this.item.key.equal_to((other_node.item.key)) && this._value_less_than(other_node)\n }\n }\n\n _value_equal(other_node) {\n return this.item.value && other_node.item.value && this.item.value.equal_to ?\n this.item.value.equal_to(other_node.item.value) :\n this.item.value === other_node.item.value;\n }\n equal_to(other_node) {\n // if tree stores only keys\n if (this.item.value === this.item.key && other_node.item.value === other_node.item.key) {\n return this.item.key.equal_to(other_node.item.key);\n }\n else { // if tree stores keys and values\n return this.item.key.equal_to(other_node.item.key) && this._value_equal(other_node);\n }\n }\n\n intersect(other_node) {\n return this.item.key.intersect(other_node.item.key);\n }\n\n copy_data(other_node) {\n this.item.key = other_node.item.key;\n this.item.value = other_node.item.value;\n }\n\n update_max() {\n // use key (Interval) max property instead of key.high\n this.max = this.item.key ? this.item.key.max : undefined;\n if (this.right && this.right.max) {\n const comparable_max = this.item.key.constructor.comparable_max; // static method\n this.max = comparable_max(this.max, this.right.max);\n }\n if (this.left && this.left.max) {\n const comparable_max = this.item.key.constructor.comparable_max; // static method\n this.max = comparable_max(this.max, this.left.max);\n }\n }\n\n // Other_node does not intersect any node of left subtree, if this.left.max < other_node.item.key.low\n not_intersect_left_subtree(search_node) {\n const comparable_less_than = this.item.key.constructor.comparable_less_than; // static method\n let high = this.left.max.high !== undefined ? this.left.max.high : this.left.max;\n return comparable_less_than(high, search_node.item.key.low);\n }\n\n // Other_node does not intersect right subtree if other_node.item.key.high < this.right.key.low\n not_intersect_right_subtree(search_node) {\n const comparable_less_than = this.item.key.constructor.comparable_less_than; // static method\n let low = this.right.max.low !== undefined ? this.right.max.low : this.right.item.key.low;\n return comparable_less_than(search_node.item.key.high, low);\n }\n}\n\n/\n Created by Alex Bol on 3/31/2017.\n /\n\n// const nil_node = new Node();\n\n/\n Implementation of interval binary search tree <br/>\n * Interval tree stores items which are couples of {key:interval, value: value} <br/>\n * Interval is an object with high and low properties or simply pair [low,high] of numeric values <br />\n * @type {IntervalTree}\n /\nclass IntervalTree {\n /\n Construct new empty instance of IntervalTree\n /\n constructor() {\n this.root = null;\n this.nil_node = new Node();\n }\n\n /\n Returns number of items stored in the interval tree\n * @returns {number}\n /\n get size() {\n let count = 0;\n this.tree_walk(this.root, () => count++);\n return count;\n }\n\n /\n Returns array of sorted keys in the ascending order\n * @returns {Array}\n /\n get keys() {\n let res = [];\n this.tree_walk(this.root, (node) => res.push(\n node.item.key.output ? node.item.key.output() : node.item.key\n ));\n return res;\n }\n\n /\n Return array of values in the ascending keys order\n * @returns {Array}\n /\n get values() {\n let res = [];\n this.tree_walk(this.root, (node) => res.push(node.item.value));\n return res;\n }\n\n /\n Returns array of items (<key,value> pairs) in the ascended keys order\n * @returns {Array}\n /\n get items() {\n let res = [];\n this.tree_walk(this.root, (node) => res.push({\n key: node.item.key.output ? node.item.key.output() : node.item.key,\n value: node.item.value\n }));\n return res;\n }\n\n /\n Returns true if tree is empty\n * @returns {boolean}\n /\n isEmpty() {\n return (this.root == null \|\| this.root === this.nil_node);\n }\n\n /\n Clear tree\n /\n clear() {\n this.root = null;\n }\n\n /\n Insert new item into interval tree\n * @param {Interval} key - interval object or array of two numbers [low, high]\n * @param {any} value - value representing any object (optional)\n * @returns {Node} returns reference to inserted node as an object {key:interval, value: value}\n /\n insert(key, value = key) {\n if (key === undefined) return;\n let insert_node = new Node(key, value, this.nil_node, this.nil_node, null, RB_TREE_COLOR_RED);\n this.tree_insert(insert_node);\n this.recalc_max(insert_node);\n return insert_node;\n }\n\n /\n Returns true if item {key,value} exist in the tree\n * @param {Interval} key - interval correspondent to keys stored in the tree\n * @param {any} value - value object to be checked\n * @returns {boolean} true if item {key, value} exist in the tree, false otherwise\n /\n exist(key, value = key) {\n let search_node = new Node(key, value);\n return !!this.tree_search(this.root, search_node);\n }\n\n /\n Remove entry {key, value} from the tree\n * @param {Interval} key - interval correspondent to keys stored in the tree\n * @param {any} value - value object\n * @returns {boolean} true if item {key, value} deleted, false if not found\n /\n remove(key, value = key) {\n let search_node = new Node(key, value);\n let delete_node = this.tree_search(this.root, search_node);\n if (delete_node) {\n this.tree_delete(delete_node);\n }\n return delete_node;\n }\n\n /\n Returns array of entry values which keys intersect with given interval <br/>\n * If no values stored in the tree, returns array of keys which intersect given interval\n * @param {Interval} interval - search interval, or tuple [low, high]\n * @param outputMapperFn(value,key) - optional function that maps (value, key) to custom output\n * @returns {Array}\n /\n search(interval, outputMapperFn = (value, key) => value === key ? key.output() : value) {\n let search_node = new Node(interval);\n let resp_nodes = [];\n this.tree_search_interval(this.root, search_node, resp_nodes);\n return resp_nodes.map(node => outputMapperFn(node.item.value, node.item.key))\n }\n\n /\n Returns true if intersection between given and any interval stored in the tree found\n * @param {Interval} interval - search interval or tuple [low, high]\n * @returns {boolean}\n /\n intersect_any(interval) {\n let search_node = new Node(interval);\n return this.tree_find_any_interval(this.root, search_node);\n }\n\n /\n Tree visitor. For each node implement a callback function. <br/>\n * Method calls a callback function with two parameters (key, value)\n * @param visitor(key,value) - function to be called for each tree item\n /\n forEach(visitor) {\n this.tree_walk(this.root, (node) => visitor(node.item.key, node.item.value));\n }\n\n /\n Value Mapper. Walk through every node and map node value to another value\n * @param callback(value,key) - function to be called for each tree item\n /\n map(callback) {\n const tree = new IntervalTree();\n this.tree_walk(this.root, (node) => tree.insert(node.item.key, callback(node.item.value, node.item.key)));\n return tree;\n }\n\n /\n @param {Interval} interval - optional if the iterator is intended to start from the beginning\n * @param outputMapperFn(value,key) - optional function that maps (value, key) to custom output\n * @returns {Iterator}\n /\n iterate(interval, outputMapperFn = (value, key) => value === key ? key.output() : value) {\n let node;\n if (interval) {\n node = this.tree_search_nearest_forward(this.root, new Node(interval));\n } else if (this.root) {\n node = this.local_minimum(this.root);\n }\n while (node) {\n yield outputMapperFn(node.item.value, node.item.key);\n node = this.tree_successor(node);\n }\n }\n\n recalc_max(node) {\n let node_current = node;\n while (node_current.parent != null) {\n node_current.parent.update_max();\n node_current = node_current.parent;\n }\n }\n\n tree_insert(insert_node) {\n let current_node = this.root;\n let parent_node = null;\n\n if (this.root == null \|\| this.root === this.nil_node) {\n this.root = insert_node;\n }\n else {\n while (current_node !== this.nil_node) {\n parent_node = current_node;\n if (insert_node.less_than(current_node)) {\n current_node = current_node.left;\n }\n else {\n current_node = current_node.right;\n }\n }\n\n insert_node.parent = parent_node;\n\n if (insert_node.less_than(parent_node)) {\n parent_node.left = insert_node;\n }\n else {\n parent_node.right = insert_node;\n }\n }\n\n this.insert_fixup(insert_node);\n }\n\n// After insertion insert_node may have red-colored parent, and this is a single possible violation\n// Go upwords to the root and re-color until violation will be resolved\n insert_fixup(insert_node) {\n let current_node;\n let uncle_node;\n\n current_node = insert_node;\n while (current_node !== this.root && current_node.parent.color === RB_TREE_COLOR_RED) {\n if (current_node.parent === current_node.parent.parent.left) { // parent is left child of grandfather\n uncle_node = current_node.parent.parent.right; // right brother of parent\n if (uncle_node.color === RB_TREE_COLOR_RED) { // Case 1. Uncle is red\n // re-color father and uncle into black\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n uncle_node.color = RB_TREE_COLOR_BLACK;\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n current_node = current_node.parent.parent;\n }\n else { // Case 2 & 3. Uncle is black\n if (current_node === current_node.parent.right) { // Case 2. Current if right child\n // This case is transformed into Case 3.\n current_node = current_node.parent;\n this.rotate_left(current_node);\n }\n current_node.parent.color = RB_TREE_COLOR_BLACK; // Case 3. Current is left child.\n // Re-color father and grandfather, rotate grandfather right\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n this.rotate_right(current_node.parent.parent);\n }\n }\n else { // parent is right child of grandfather\n uncle_node = current_node.parent.parent.left; // left brother of parent\n if (uncle_node.color === RB_TREE_COLOR_RED) { // Case 4. Uncle is red\n // re-color father and uncle into black\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n uncle_node.color = RB_TREE_COLOR_BLACK;\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n current_node = current_node.parent.parent;\n }\n else {\n if (current_node === current_node.parent.left) { // Case 5. Current is left child\n // Transform into case 6\n current_node = current_node.parent;\n this.rotate_right(current_node);\n }\n current_node.parent.color = RB_TREE_COLOR_BLACK; // Case 6. Current is right child.\n // Re-color father and grandfather, rotate grandfather left\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n this.rotate_left(current_node.parent.parent);\n }\n }\n }\n\n this.root.color = RB_TREE_COLOR_BLACK;\n }\n\n tree_delete(delete_node) {\n let cut_node; // node to be cut - either delete_node or successor_node (\"y\" from 14.4)\n let fix_node; // node to fix rb tree property (\"x\" from 14.4)\n\n if (delete_node.left === this.nil_node \|\| delete_node.right === this.nil_node) { // delete_node has less then 2 children\n cut_node = delete_node;\n }\n else { // delete_node has 2 children\n cut_node = this.tree_successor(delete_node);\n }\n\n // fix_node if single child of cut_node\n if (cut_node.left !== this.nil_node) {\n fix_node = cut_node.left;\n }\n else {\n fix_node = cut_node.right;\n }\n\n // remove cut_node from parent\n /if (fix_node != this.nil_node) {/\n fix_node.parent = cut_node.parent;\n /}/\n\n if (cut_node === this.root) {\n this.root = fix_node;\n }\n else {\n if (cut_node === cut_node.parent.left) {\n cut_node.parent.left = fix_node;\n }\n else {\n cut_node.parent.right = fix_node;\n }\n cut_node.parent.update_max(); // update max property of the parent\n }\n\n this.recalc_max(fix_node); // update max property upward from fix_node to root\n\n // COPY DATA !!!\n // Delete_node becomes cut_node, it means that we cannot hold reference\n // to node in outer structure and we will have to delete by key, additional search need\n if (cut_node !== delete_node) {\n delete_node.copy_data(cut_node);\n delete_node.update_max(); // update max property of the cut node at the new place\n this.recalc_max(delete_node); // update max property upward from delete_node to root\n }\n\n if (/fix_node != this.nil_node && /cut_node.color === RB_TREE_COLOR_BLACK) {\n this.delete_fixup(fix_node);\n }\n }\n\n delete_fixup(fix_node) {\n let current_node = fix_node;\n let brother_node;\n\n while (current_node !== this.root && current_node.parent != null && current_node.color === RB_TREE_COLOR_BLACK) {\n if (current_node === current_node.parent.left) { // fix node is left child\n brother_node = current_node.parent.right;\n if (brother_node.color === RB_TREE_COLOR_RED) { // Case 1. Brother is red\n brother_node.color = RB_TREE_COLOR_BLACK; // re-color brother\n current_node.parent.color = RB_TREE_COLOR_RED; // re-color father\n this.rotate_left(current_node.parent);\n brother_node = current_node.parent.right; // update brother\n }\n // Derive to cases 2..4: brother is black\n if (brother_node.left.color === RB_TREE_COLOR_BLACK &&\n brother_node.right.color === RB_TREE_COLOR_BLACK) { // case 2: both nephews black\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n current_node = current_node.parent; // continue iteration\n }\n else {\n if (brother_node.right.color === RB_TREE_COLOR_BLACK) { // case 3: left nephew red, right nephew black\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n brother_node.left.color = RB_TREE_COLOR_BLACK; // re-color nephew\n this.rotate_right(brother_node);\n brother_node = current_node.parent.right; // update brother\n // Derive to case 4: left nephew black, right nephew red\n }\n // case 4: left nephew black, right nephew red\n brother_node.color = current_node.parent.color;\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n brother_node.right.color = RB_TREE_COLOR_BLACK;\n this.rotate_left(current_node.parent);\n current_node = this.root; // exit from loop\n }\n }\n else { // fix node is right child\n brother_node = current_node.parent.left;\n if (brother_node.color === RB_TREE_COLOR_RED) { // Case 1. Brother is red\n brother_node.color = RB_TREE_COLOR_BLACK; // re-color brother\n current_node.parent.color = RB_TREE_COLOR_RED; // re-color father\n this.rotate_right(current_node.parent);\n brother_node = current_node.parent.left; // update brother\n }\n // Go to cases 2..4\n if (brother_node.left.color === RB_TREE_COLOR_BLACK &&\n brother_node.right.color === RB_TREE_COLOR_BLACK) { // case 2\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n current_node = current_node.parent; // continue iteration\n }\n else {\n if (brother_node.left.color === RB_TREE_COLOR_BLACK) { // case 3: right nephew red, left nephew black\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n brother_node.right.color = RB_TREE_COLOR_BLACK; // re-color nephew\n this.rotate_left(brother_node);\n brother_node = current_node.parent.left; // update brother\n // Derive to case 4: right nephew black, left nephew red\n }\n // case 4: right nephew black, left nephew red\n brother_node.color = current_node.parent.color;\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n brother_node.left.color = RB_TREE_COLOR_BLACK;\n this.rotate_right(current_node.parent);\n current_node = this.root; // force exit from loop\n }\n }\n }\n\n current_node.color = RB_TREE_COLOR_BLACK;\n }\n\n tree_search(node, search_node) {\n if (node == null \|\| node === this.nil_node)\n return undefined;\n\n if (search_node.equal_to(node)) {\n return node;\n }\n if (search_node.less_than(node)) {\n return this.tree_search(node.left, search_node);\n }\n else {\n return this.tree_search(node.right, search_node);\n }\n }\n\n tree_search_nearest_forward(node, search_node) {\n let best;\n let curr = node;\n while (curr && curr !== this.nil_node) {\n if (curr.less_than(search_node)) {\n if (curr.intersect(search_node)) {\n best = curr;\n curr = curr.left;\n } else {\n curr = curr.right;\n }\n } else {\n if (!best \|\| curr.less_than(best)) best = curr;\n curr = curr.left;\n }\n }\n return best \|\| null;\n }\n\n // Original search_interval method; container res support push() insertion\n // Search all intervals intersecting given one\n tree_search_interval(node, search_node, res) {\n if (node != null && node !== this.nil_node) {\n // if (node->left != this.nil_node && node->left->max >= low) {\n if (node.left !== this.nil_node && !node.not_intersect_left_subtree(search_node)) {\n this.tree_search_interval(node.left, search_node, res);\n }\n // if (low <= node->high && node->low <= high) {\n if (node.intersect(search_node)) {\n res.push(node);\n }\n // if (node->right != this.nil_node && node->low <= high) {\n if (node.right !== this.nil_node && !node.not_intersect_right_subtree(search_node)) {\n this.tree_search_interval(node.right, search_node, res);\n }\n }\n }\n\n tree_find_any_interval(node, search_node) {\n let found = false;\n if (node != null && node !== this.nil_node) {\n if (node.left !== this.nil_node && !node.not_intersect_left_subtree(search_node)) {\n found = this.tree_find_any_interval(node.left, search_node);\n }\n if (!found) {\n found = node.intersect(search_node);\n }\n if (!found && node.right !== this.nil_node && !node.not_intersect_right_subtree(search_node)) {\n found = this.tree_find_any_interval(node.right, search_node);\n }\n }\n return found;\n }\n\n local_minimum(node) {\n let node_min = node;\n while (node_min.left != null && node_min.left !== this.nil_node) {\n node_min = node_min.left;\n }\n return node_min;\n }\n\n // not in use\n local_maximum(node) {\n let node_max = node;\n while (node_max.right != null && node_max.right !== this.nil_node) {\n node_max = node_max.right;\n }\n return node_max;\n }\n\n tree_successor(node) {\n let node_successor;\n let current_node;\n let parent_node;\n\n if (node.right !== this.nil_node) {\n node_successor = this.local_minimum(node.right);\n }\n else {\n current_node = node;\n parent_node = node.parent;\n while (parent_node != null && parent_node.right === current_node) {\n current_node = parent_node;\n parent_node = parent_node.parent;\n }\n node_successor = parent_node;\n }\n return node_successor;\n }\n\n // \| right-rotate(T,y) \|\n // y ---------------. x\n // / \\ / \\\n // x c left-rotate(T,x) a y\n // / \\ <--------------- / \\\n // a b b c\n\n rotate_left(x) {\n let y = x.right;\n\n x.right = y.left; // b goes to x.right\n\n if (y.left !== this.nil_node) {\n y.left.parent = x; // x becomes parent of b\n }\n y.parent = x.parent; // move parent\n\n if (x === this.root) {\n this.root = y; // y becomes root\n }\n else { // y becomes child of x.parent\n if (x === x.parent.left) {\n x.parent.left = y;\n }\n else {\n x.parent.right = y;\n }\n }\n y.left = x; // x becomes left child of y\n x.parent = y; // and y becomes parent of x\n\n if (x != null && x !== this.nil_node) {\n x.update_max();\n }\n\n y = x.parent;\n if (y != null && y !== this.nil_node) {\n y.update_max();\n }\n }\n\n rotate_right(y) {\n let x = y.left;\n\n y.left = x.right; // b goes to y.left\n\n if (x.right !== this.nil_node) {\n x.right.parent = y; // y becomes parent of b\n }\n x.parent = y.parent; // move parent\n\n if (y === this.root) { // x becomes root\n this.root = x;\n }\n else { // y becomes child of x.parent\n if (y === y.parent.left) {\n y.parent.left = x;\n }\n else {\n y.parent.right = x;\n }\n }\n x.right = y; 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{ 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","/**\n * Created by Alex Bol on 4/1/2017.\n */\n\n/**\n * Interval is a pair of numbers or a pair of any comparable objects on which may be defined predicates\n * *equal*, *less* and method *max(p1, p1)* that returns maximum in a pair.\n * When interval is an object rather than a pair of numbers, this object should have properties *low*, *high*, *max*\n * and implement methods *less_than(), equal_to(), intersect(), not_intersect(), clone(), output()*.\n * Two static methods *comparable_max(), comparable_less_than()* define how to compare values in pair. \n * This interface is described in typescript definition file *index.d.ts*\n *\n * Axis aligned rectangle is an example of such interval.\n * We may look at rectangle as an interval between its low left and top right corners.\n * See **Box** class in [flatten-js](https://github.com/alexbol99/flatten-js) library as the example\n * of Interval interface implementation\n * @type {Interval}\n */\nconst Interval = class Interval {\n /**\n * Accept two comparable values and creates new instance of interval\n * Predicate Interval.comparable_less(low, high) supposed to return true on these values\n * @param low\n * @param high\n */\n constructor(low, high) {\n this.low = low;\n this.high = high;\n }\n\n /**\n * Clone interval\n * @returns {Interval}\n */\n clone() {\n return new Interval(this.low, this.high);\n }\n\n /**\n * Propery max returns clone of this interval\n * @returns {Interval}\n */\n get max() {\n return this.clone(); // this.high;\n }\n\n /**\n * Predicate returns true is this interval less than other interval\n * @param other_interval\n * @returns {boolean}\n */\n less_than(other_interval) {\n return this.low < other_interval.low ||\n this.low === other_interval.low && this.high < other_interval.high;\n }\n\n /**\n * Predicate returns true is this interval equals to other interval\n * @param other_interval\n * @returns {boolean}\n */\n equal_to(other_interval) {\n return this.low === other_interval.low && this.high === other_interval.high;\n }\n\n /**\n * Predicate returns true if this interval intersects other interval\n * @param other_interval\n * @returns {boolean}\n */\n intersect(other_interval) {\n return !this.not_intersect(other_interval);\n }\n\n /**\n * Predicate returns true if this interval does not intersect other interval\n * @param other_interval\n * @returns {boolean}\n */\n not_intersect(other_interval) {\n return (this.high < other_interval.low || other_interval.high < this.low);\n }\n\n /**\n * Returns new interval merged with other interval\n * @param {Interval} other_interval - Other interval to merge with\n * @returns {Interval}\n */\n merge(other_interval) {\n return new Interval(\n this.low === undefined ?\n other_interval.low : (this.low < other_interval.low ? this.low : other_interval.low),\n this.high === undefined ?\n other_interval.high : (this.high > other_interval.high ? this.high : other_interval.high)\n );\n }\n\n /**\n * Returns how key should return\n */\n output() {\n return [this.low, this.high];\n }\n\n /**\n * Function returns maximum between two comparable values\n * @param interval1\n * @param interval2\n * @returns {Interval}\n */\n static comparable_max(interval1, interval2) {\n return interval1.merge(interval2);\n }\n\n /**\n * Predicate returns true if first value less than second value\n * @param val1\n * @param val2\n * @returns {boolean}\n */\n static comparable_less_than(val1, val2 ) {\n return val1 < val2;\n }\n};\n\n/**\n * Created by Alex Bol on 3/28/2017.\n */\n\n\n// module.exports = {\n// RB_TREE_COLOR_RED: 0,\n// RB_TREE_COLOR_BLACK: 1\n// };\n\nconst RB_TREE_COLOR_RED = 0;\nconst RB_TREE_COLOR_BLACK = 1;\n\n/**\n * Created by Alex Bol on 4/1/2017.\n */\n\n\nclass Node {\n constructor(key = undefined, value = undefined,\n left = null, right = null, parent = null, color = RB_TREE_COLOR_BLACK) {\n this.left = left; // reference to left child node\n this.right = right; // reference to right child node\n this.parent = parent; // reference to parent node\n this.color = color;\n\n this.item = {key: key, value: value}; // key is supposed to be instance of Interval\n\n /* If not, this should by an array of two numbers */\n if (key && key instanceof Array && key.length === 2) {\n if (!Number.isNaN(key[0]) && !Number.isNaN(key[1])) {\n let [low, high] = key;\n if (low > high) [low, high] = [high, low];\n this.item.key = new Interval(low, high);\n }\n }\n\n this.max = this.item.key ? this.item.key.max : undefined;\n }\n\n isNil() {\n return (this.item.key === undefined && this.item.value === undefined &&\n this.left === null && this.right === null && this.color === RB_TREE_COLOR_BLACK);\n }\n\n _value_less_than(other_node) {\n return this.item.value && other_node.item.value && this.item.value.less_than ?\n this.item.value.less_than(other_node.item.value) :\n this.item.value < other_node.item.value;\n }\n\n less_than(other_node) {\n // if tree stores only keys\n if (this.item.value === this.item.key && other_node.item.value === other_node.item.key) {\n return this.item.key.less_than(other_node.item.key);\n }\n else { // if tree stores keys and values\n return this.item.key.less_than(other_node.item.key) ||\n this.item.key.equal_to((other_node.item.key)) && this._value_less_than(other_node)\n }\n }\n\n _value_equal(other_node) {\n return this.item.value && other_node.item.value && this.item.value.equal_to ?\n this.item.value.equal_to(other_node.item.value) :\n this.item.value === other_node.item.value;\n }\n equal_to(other_node) {\n // if tree stores only keys\n if (this.item.value === this.item.key && other_node.item.value === other_node.item.key) {\n return this.item.key.equal_to(other_node.item.key);\n }\n else { // if tree stores keys and values\n return this.item.key.equal_to(other_node.item.key) && this._value_equal(other_node);\n }\n }\n\n intersect(other_node) {\n return this.item.key.intersect(other_node.item.key);\n }\n\n copy_data(other_node) {\n this.item.key = other_node.item.key;\n this.item.value = other_node.item.value;\n }\n\n update_max() {\n // use key (Interval) max property instead of key.high\n this.max = this.item.key ? this.item.key.max : undefined;\n if (this.right && this.right.max) {\n const comparable_max = this.item.key.constructor.comparable_max; // static method\n this.max = comparable_max(this.max, this.right.max);\n }\n if (this.left && this.left.max) {\n const comparable_max = this.item.key.constructor.comparable_max; // static method\n this.max = comparable_max(this.max, this.left.max);\n }\n }\n\n // Other_node does not intersect any node of left subtree, if this.left.max < other_node.item.key.low\n not_intersect_left_subtree(search_node) {\n const comparable_less_than = this.item.key.constructor.comparable_less_than; // static method\n let high = this.left.max.high !== undefined ? this.left.max.high : this.left.max;\n return comparable_less_than(high, search_node.item.key.low);\n }\n\n // Other_node does not intersect right subtree if other_node.item.key.high < this.right.key.low\n not_intersect_right_subtree(search_node) {\n const comparable_less_than = this.item.key.constructor.comparable_less_than; // static method\n let low = this.right.max.low !== undefined ? this.right.max.low : this.right.item.key.low;\n return comparable_less_than(search_node.item.key.high, low);\n }\n}\n\n/**\n * Created by Alex Bol on 3/31/2017.\n */\n\n// const nil_node = new Node();\n\n/**\n * Implementation of interval binary search tree \n * Interval tree stores items which are couples of {key:interval, value: value} \n * Interval is an object with high and low properties or simply pair [low,high] of numeric values \n * @type {IntervalTree}\n */\nclass IntervalTree {\n /**\n * Construct new empty instance of IntervalTree\n */\n constructor() {\n this.root = null;\n this.nil_node = new Node();\n }\n\n /**\n * Returns number of items stored in the interval tree\n * @returns {number}\n */\n get size() {\n let count = 0;\n this.tree_walk(this.root, () => count++);\n return count;\n }\n\n /**\n * Returns array of sorted keys in the ascending order\n * @returns {Array}\n */\n get keys() {\n let res = [];\n this.tree_walk(this.root, (node) => res.push(\n node.item.key.output ? node.item.key.output() : node.item.key\n ));\n return res;\n }\n\n /**\n * Return array of values in the ascending keys order\n * @returns {Array}\n */\n get values() {\n let res = [];\n this.tree_walk(this.root, (node) => res.push(node.item.value));\n return res;\n }\n\n /**\n * Returns array of items (<key,value> pairs) in the ascended keys order\n * @returns {Array}\n */\n get items() {\n let res = [];\n this.tree_walk(this.root, (node) => res.push({\n key: node.item.key.output ? node.item.key.output() : node.item.key,\n value: node.item.value\n }));\n return res;\n }\n\n /**\n * Returns true if tree is empty\n * @returns {boolean}\n */\n isEmpty() {\n return (this.root == null || this.root === this.nil_node);\n }\n\n /**\n * Clear tree\n */\n clear() {\n this.root = null;\n }\n\n /**\n * Insert new item into interval tree\n * @param {Interval} key - interval object or array of two numbers [low, high]\n * @param {any} value - value representing any object (optional)\n * @returns {Node} returns reference to inserted node as an object {key:interval, value: value}\n */\n insert(key, value = key) {\n if (key === undefined) return;\n let insert_node = new Node(key, value, this.nil_node, this.nil_node, null, RB_TREE_COLOR_RED);\n this.tree_insert(insert_node);\n this.recalc_max(insert_node);\n return insert_node;\n }\n\n /**\n * Returns true if item {key,value} exist in the tree\n * @param {Interval} key - interval correspondent to keys stored in the tree\n * @param {any} value - value object to be checked\n * @returns {boolean} true if item {key, value} exist in the tree, false otherwise\n */\n exist(key, value = key) {\n let search_node = new Node(key, value);\n return !!this.tree_search(this.root, search_node);\n }\n\n /**\n * Remove entry {key, value} from the tree\n * @param {Interval} key - interval correspondent to keys stored in the tree\n * @param {any} value - value object\n * @returns {boolean} true if item {key, value} deleted, false if not found\n */\n remove(key, value = key) {\n let search_node = new Node(key, value);\n let delete_node = this.tree_search(this.root, search_node);\n if (delete_node) {\n this.tree_delete(delete_node);\n }\n return delete_node;\n }\n\n /**\n * Returns array of entry values which keys intersect with given interval \n * If no values stored in the tree, returns array of keys which intersect given interval\n * @param {Interval} interval - search interval, or tuple [low, high]\n * @param outputMapperFn(value,key) - optional function that maps (value, key) to custom output\n * @returns {Array}\n */\n search(interval, outputMapperFn = (value, key) => value === key ? key.output() : value) {\n let search_node = new Node(interval);\n let resp_nodes = [];\n this.tree_search_interval(this.root, search_node, resp_nodes);\n return resp_nodes.map(node => outputMapperFn(node.item.value, node.item.key))\n }\n\n /**\n * Returns true if intersection between given and any interval stored in the tree found\n * @param {Interval} interval - search interval or tuple [low, high]\n * @returns {boolean}\n */\n intersect_any(interval) {\n let search_node = new Node(interval);\n return this.tree_find_any_interval(this.root, search_node);\n }\n\n /**\n * Tree visitor. For each node implement a callback function. \n * Method calls a callback function with two parameters (key, value)\n * @param visitor(key,value) - function to be called for each tree item\n */\n forEach(visitor) {\n this.tree_walk(this.root, (node) => visitor(node.item.key, node.item.value));\n }\n\n /**\n * Value Mapper. Walk through every node and map node value to another value\n * @param callback(value,key) - function to be called for each tree item\n */\n map(callback) {\n const tree = new IntervalTree();\n this.tree_walk(this.root, (node) => tree.insert(node.item.key, callback(node.item.value, node.item.key)));\n return tree;\n }\n\n /**\n * @param {Interval} interval - optional if the iterator is intended to start from the beginning\n * @param outputMapperFn(value,key) - optional function that maps (value, key) to custom output\n * @returns {Iterator}\n */\n *iterate(interval, outputMapperFn = (value, key) => value === key ? key.output() : value) {\n let node;\n if (interval) {\n node = this.tree_search_nearest_forward(this.root, new Node(interval));\n } else if (this.root) {\n node = this.local_minimum(this.root);\n }\n while (node) {\n yield outputMapperFn(node.item.value, node.item.key);\n node = this.tree_successor(node);\n }\n }\n\n recalc_max(node) {\n let node_current = node;\n while (node_current.parent != null) {\n node_current.parent.update_max();\n node_current = node_current.parent;\n }\n }\n\n tree_insert(insert_node) {\n let current_node = this.root;\n let parent_node = null;\n\n if (this.root == null || this.root === this.nil_node) {\n this.root = insert_node;\n }\n else {\n while (current_node !== this.nil_node) {\n parent_node = current_node;\n if (insert_node.less_than(current_node)) {\n current_node = current_node.left;\n }\n else {\n current_node = current_node.right;\n }\n }\n\n insert_node.parent = parent_node;\n\n if (insert_node.less_than(parent_node)) {\n parent_node.left = insert_node;\n }\n else {\n parent_node.right = insert_node;\n }\n }\n\n this.insert_fixup(insert_node);\n }\n\n// After insertion insert_node may have red-colored parent, and this is a single possible violation\n// Go upwords to the root and re-color until violation will be resolved\n insert_fixup(insert_node) {\n let current_node;\n let uncle_node;\n\n current_node = insert_node;\n while (current_node !== this.root && current_node.parent.color === RB_TREE_COLOR_RED) {\n if (current_node.parent === current_node.parent.parent.left) { // parent is left child of grandfather\n uncle_node = current_node.parent.parent.right; // right brother of parent\n if (uncle_node.color === RB_TREE_COLOR_RED) { // Case 1. Uncle is red\n // re-color father and uncle into black\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n uncle_node.color = RB_TREE_COLOR_BLACK;\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n current_node = current_node.parent.parent;\n }\n else { // Case 2 & 3. Uncle is black\n if (current_node === current_node.parent.right) { // Case 2. Current if right child\n // This case is transformed into Case 3.\n current_node = current_node.parent;\n this.rotate_left(current_node);\n }\n current_node.parent.color = RB_TREE_COLOR_BLACK; // Case 3. Current is left child.\n // Re-color father and grandfather, rotate grandfather right\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n this.rotate_right(current_node.parent.parent);\n }\n }\n else { // parent is right child of grandfather\n uncle_node = current_node.parent.parent.left; // left brother of parent\n if (uncle_node.color === RB_TREE_COLOR_RED) { // Case 4. Uncle is red\n // re-color father and uncle into black\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n uncle_node.color = RB_TREE_COLOR_BLACK;\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n current_node = current_node.parent.parent;\n }\n else {\n if (current_node === current_node.parent.left) { // Case 5. Current is left child\n // Transform into case 6\n current_node = current_node.parent;\n this.rotate_right(current_node);\n }\n current_node.parent.color = RB_TREE_COLOR_BLACK; // Case 6. Current is right child.\n // Re-color father and grandfather, rotate grandfather left\n current_node.parent.parent.color = RB_TREE_COLOR_RED;\n this.rotate_left(current_node.parent.parent);\n }\n }\n }\n\n this.root.color = RB_TREE_COLOR_BLACK;\n }\n\n tree_delete(delete_node) {\n let cut_node; // node to be cut - either delete_node or successor_node (\"y\" from 14.4)\n let fix_node; // node to fix rb tree property (\"x\" from 14.4)\n\n if (delete_node.left === this.nil_node || delete_node.right === this.nil_node) { // delete_node has less then 2 children\n cut_node = delete_node;\n }\n else { // delete_node has 2 children\n cut_node = this.tree_successor(delete_node);\n }\n\n // fix_node if single child of cut_node\n if (cut_node.left !== this.nil_node) {\n fix_node = cut_node.left;\n }\n else {\n fix_node = cut_node.right;\n }\n\n // remove cut_node from parent\n /*if (fix_node != this.nil_node) {*/\n fix_node.parent = cut_node.parent;\n /*}*/\n\n if (cut_node === this.root) {\n this.root = fix_node;\n }\n else {\n if (cut_node === cut_node.parent.left) {\n cut_node.parent.left = fix_node;\n }\n else {\n cut_node.parent.right = fix_node;\n }\n cut_node.parent.update_max(); // update max property of the parent\n }\n\n this.recalc_max(fix_node); // update max property upward from fix_node to root\n\n // COPY DATA !!!\n // Delete_node becomes cut_node, it means that we cannot hold reference\n // to node in outer structure and we will have to delete by key, additional search need\n if (cut_node !== delete_node) {\n delete_node.copy_data(cut_node);\n delete_node.update_max(); // update max property of the cut node at the new place\n this.recalc_max(delete_node); // update max property upward from delete_node to root\n }\n\n if (/*fix_node != this.nil_node && */cut_node.color === RB_TREE_COLOR_BLACK) {\n this.delete_fixup(fix_node);\n }\n }\n\n delete_fixup(fix_node) {\n let current_node = fix_node;\n let brother_node;\n\n while (current_node !== this.root && current_node.parent != null && current_node.color === RB_TREE_COLOR_BLACK) {\n if (current_node === current_node.parent.left) { // fix node is left child\n brother_node = current_node.parent.right;\n if (brother_node.color === RB_TREE_COLOR_RED) { // Case 1. Brother is red\n brother_node.color = RB_TREE_COLOR_BLACK; // re-color brother\n current_node.parent.color = RB_TREE_COLOR_RED; // re-color father\n this.rotate_left(current_node.parent);\n brother_node = current_node.parent.right; // update brother\n }\n // Derive to cases 2..4: brother is black\n if (brother_node.left.color === RB_TREE_COLOR_BLACK &&\n brother_node.right.color === RB_TREE_COLOR_BLACK) { // case 2: both nephews black\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n current_node = current_node.parent; // continue iteration\n }\n else {\n if (brother_node.right.color === RB_TREE_COLOR_BLACK) { // case 3: left nephew red, right nephew black\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n brother_node.left.color = RB_TREE_COLOR_BLACK; // re-color nephew\n this.rotate_right(brother_node);\n brother_node = current_node.parent.right; // update brother\n // Derive to case 4: left nephew black, right nephew red\n }\n // case 4: left nephew black, right nephew red\n brother_node.color = current_node.parent.color;\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n brother_node.right.color = RB_TREE_COLOR_BLACK;\n this.rotate_left(current_node.parent);\n current_node = this.root; // exit from loop\n }\n }\n else { // fix node is right child\n brother_node = current_node.parent.left;\n if (brother_node.color === RB_TREE_COLOR_RED) { // Case 1. Brother is red\n brother_node.color = RB_TREE_COLOR_BLACK; // re-color brother\n current_node.parent.color = RB_TREE_COLOR_RED; // re-color father\n this.rotate_right(current_node.parent);\n brother_node = current_node.parent.left; // update brother\n }\n // Go to cases 2..4\n if (brother_node.left.color === RB_TREE_COLOR_BLACK &&\n brother_node.right.color === RB_TREE_COLOR_BLACK) { // case 2\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n current_node = current_node.parent; // continue iteration\n }\n else {\n if (brother_node.left.color === RB_TREE_COLOR_BLACK) { // case 3: right nephew red, left nephew black\n brother_node.color = RB_TREE_COLOR_RED; // re-color brother\n brother_node.right.color = RB_TREE_COLOR_BLACK; // re-color nephew\n this.rotate_left(brother_node);\n brother_node = current_node.parent.left; // update brother\n // Derive to case 4: right nephew black, left nephew red\n }\n // case 4: right nephew black, left nephew red\n brother_node.color = current_node.parent.color;\n current_node.parent.color = RB_TREE_COLOR_BLACK;\n brother_node.left.color = RB_TREE_COLOR_BLACK;\n this.rotate_right(current_node.parent);\n current_node = this.root; // force exit from loop\n }\n }\n }\n\n current_node.color = RB_TREE_COLOR_BLACK;\n }\n\n tree_search(node, search_node) {\n if (node == null || node === this.nil_node)\n return undefined;\n\n if (search_node.equal_to(node)) {\n return node;\n }\n if (search_node.less_than(node)) {\n return this.tree_search(node.left, search_node);\n }\n else {\n return this.tree_search(node.right, search_node);\n }\n }\n\n tree_search_nearest_forward(node, search_node) {\n let best;\n let curr = node;\n while (curr && curr !== this.nil_node) {\n if (curr.less_than(search_node)) {\n if (curr.intersect(search_node)) {\n best = curr;\n curr = curr.left;\n } else {\n curr = curr.right;\n }\n } else {\n if (!best || curr.less_than(best)) best = curr;\n curr = curr.left;\n }\n }\n return best || null;\n }\n\n // Original search_interval method; container res support push() insertion\n // Search all intervals intersecting given one\n tree_search_interval(node, search_node, res) {\n if (node != null && node !== this.nil_node) {\n // if (node->left != this.nil_node && node->left->max >= low) {\n if (node.left !== this.nil_node && !node.not_intersect_left_subtree(search_node)) {\n this.tree_search_interval(node.left, search_node, res);\n }\n // if (low <= node->high && node->low <= high) {\n if (node.intersect(search_node)) {\n res.push(node);\n }\n // if (node->right != this.nil_node && node->low <= high) {\n if (node.right !== this.nil_node && !node.not_intersect_right_subtree(search_node)) {\n this.tree_search_interval(node.right, search_node, res);\n }\n }\n }\n\n tree_find_any_interval(node, search_node) {\n let found = false;\n if (node != null && node !== this.nil_node) {\n if (node.left !== this.nil_node && !node.not_intersect_left_subtree(search_node)) {\n found = this.tree_find_any_interval(node.left, search_node);\n }\n if (!found) {\n found = node.intersect(search_node);\n }\n if (!found && node.right !== this.nil_node && !node.not_intersect_right_subtree(search_node)) {\n found = this.tree_find_any_interval(node.right, search_node);\n }\n }\n return found;\n }\n\n local_minimum(node) {\n let node_min = node;\n while (node_min.left != null && node_min.left !== this.nil_node) {\n node_min = node_min.left;\n }\n return node_min;\n }\n\n // not in use\n local_maximum(node) {\n let node_max = node;\n while (node_max.right != null && node_max.right !== this.nil_node) {\n node_max = node_max.right;\n }\n return node_max;\n }\n\n tree_successor(node) {\n let node_successor;\n let current_node;\n let parent_node;\n\n if (node.right !== this.nil_node) {\n node_successor = this.local_minimum(node.right);\n }\n else {\n current_node = node;\n parent_node = node.parent;\n while (parent_node != null && parent_node.right === current_node) {\n current_node = parent_node;\n parent_node = parent_node.parent;\n }\n node_successor = parent_node;\n }\n return node_successor;\n }\n\n // | right-rotate(T,y) |\n // y ---------------. x\n // / \\ / \\\n // x c left-rotate(T,x) a y\n // / \\ <--------------- / \\\n // a b b c\n\n rotate_left(x) {\n let y = x.right;\n\n x.right = y.left; // b goes to x.right\n\n if (y.left !== this.nil_node) {\n y.left.parent = x; // x becomes parent of b\n }\n y.parent = x.parent; // move parent\n\n if (x === this.root) {\n this.root = y; // y becomes root\n }\n else { // y becomes child of x.parent\n if (x === x.parent.left) {\n x.parent.left = y;\n }\n else {\n x.parent.right = y;\n }\n }\n y.left = x; // x becomes left child of y\n x.parent = y; // and y becomes parent of x\n\n if (x != null && x !== this.nil_node) {\n x.update_max();\n }\n\n y = x.parent;\n if (y != null && y !== this.nil_node) {\n y.update_max();\n }\n }\n\n rotate_right(y) {\n let x = y.left;\n\n y.left = x.right; // b goes to y.left\n\n if (x.right !== this.nil_node) {\n x.right.parent = y; // y becomes parent of b\n }\n x.parent = y.parent; // move parent\n\n if (y === this.root) { // x becomes root\n this.root = x;\n }\n else { // y becomes child of x.parent\n if (y === y.parent.left) {\n y.parent.left = x;\n }\n else {\n y.parent.right = x;\n }\n }\n x.right = y; // y becomes right child of x\n y.parent = x; // and x becomes parent of y\n\n if (y !== null && y !== this.nil_node) {\n y.update_max();\n }\n\n x = y.parent;\n if (x != null && x !== this.nil_node) {\n x.update_max();\n }\n }\n\n tree_walk(node, action) {\n if (node != null && node !== this.nil_node) {\n this.tree_walk(node.left, action);\n // arr.push(node.toArray());\n action(node);\n this.tree_walk(node.right, action);\n }\n }\n\n /* Return true if all red nodes have exactly two black child nodes */\n testRedBlackProperty() {\n let res = true;\n this.tree_walk(this.root, function (node) {\n if (node.color === RB_TREE_COLOR_RED) {\n if (!(node.left.color === RB_TREE_COLOR_BLACK && node.right.color === RB_TREE_COLOR_BLACK)) {\n res = false;\n }\n }\n });\n return res;\n }\n\n /* Throw error if not every path from root to bottom has same black height */\n testBlackHeightProperty(node) {\n let height = 0;\n let heightLeft = 0;\n let heightRight = 0;\n if (node.color === RB_TREE_COLOR_BLACK) {\n height++;\n }\n if (node.left !== this.nil_node) {\n heightLeft = this.testBlackHeightProperty(node.left);\n }\n else {\n heightLeft = 1;\n }\n if (node.right !== this.nil_node) {\n heightRight = this.testBlackHeightProperty(node.right);\n }\n else {\n heightRight = 1;\n }\n if (heightLeft !== heightRight) {\n throw new Error('Red-black height property violated');\n }\n height += heightLeft;\n return height;\n }\n}\n\nexport { Interval, Node, IntervalTree as default };\n"],"names":["async","unzip","inputData","strm","pos","i","chunks","inflator","totalSize","remainingInput","subarray","Inflate","push","Z_SYNC_FLUSH","err","Error","msg","next_in","result","length","avail_in","Uint8Array","offset","set","from","e","match","unzipChunkSlice","chunk","minv","maxv","cpos","blockPosition","dpos","dataPosition","cpositions","dpositions","buffer","len","origCpos","GziIndex","constructor","filehandle","path","this","TypeError","_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","entry","nextEntry","nextUncompressedPosition","Infinity","lowerBound","upperBound","searchPosition","Math","floor","comparison","ceil","BgzFilehandle","gziFilehandle","gziPath","gzi","stat","compressedStat","Object","assign","size","getUncompressedFileSize","blocks","undefined","blksize","bytesRead","readUInt32LE","_readAndUncompressBlock","blockBuffer","nextCompressedPosition","next","blockCompressedLength","blockPositions","destinationOffset","blockNum","uncompressedBuffer","sourceOffset","sourceEnd","min","copy","Interval","low","high","clone","max","less_than","other_interval","equal_to","intersect","not_intersect","merge","output","comparable_max","interval1","interval2","comparable_less_than","val1","val2","Node","key","value","left","right","parent","color","item","isNaN","isNil","_value_less_than","other_node","_value_equal","copy_data","update_max","not_intersect_left_subtree","search_node","not_intersect_right_subtree","IntervalTree","root","nil_node","count","tree_walk","keys","res","node","values","items","isEmpty","clear","insert","insert_node","tree_insert","recalc_max","exist","tree_search","remove","delete_node","tree_delete","search","interval","outputMapperFn","resp_nodes","tree_search_interval","map","intersect_any","tree_find_any_interval","forEach","visitor","callback","tree","iterate","tree_search_nearest_forward","local_minimum","tree_successor","node_current","current_node","parent_node","insert_fixup","uncle_node","rotate_left","rotate_right","cut_node","fix_node","delete_fixup","brother_node","best","curr","found","node_min","local_maximum","node_max","node_successor","x","y","action","testRedBlackProperty","testBlackHeightProperty","height","heightLeft","heightRight"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

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