@gmod/cram 1.6.3 → 1.7.0

package/dist/io/remoteFile.js

@@ -1,143 +0,0 @@
-"use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-var cross_fetch_1 = __importDefault(require("cross-fetch"));
-var bufferCache_1 = __importDefault(require("./bufferCache"));
-var RemoteFile = /** @class */ (function () {
-    function RemoteFile(source) {
-        var _this = this;
-        this.position = 0;
-        this.url = source;
-        this.cache = new bufferCache_1.default({
-            fetch: function (start, length) { return _this._fetch(start, length); },
-        });
-    }
-    RemoteFile.prototype._fetch = function (position, length) {
-        return __awaiter(this, void 0, void 0, function () {
-            var headers, response, nodeBuffer, _a, _b, sizeMatch;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
-                    case 0:
-                        headers = {};
-                        if (length < Infinity) {
-                            headers.range = "bytes=".concat(position, "-").concat(position + length);
-                        }
-                        else if (length === Infinity && position !== 0) {
-                            headers.range = "bytes=".concat(position, "-");
-                        }
-                        return [4 /*yield*/, (0, cross_fetch_1.default)(this.url, {
-                                method: 'GET',
-                                headers: headers,
-                                redirect: 'follow',
-                                mode: 'cors',
-                            })];
-                    case 1:
-                        response = _c.sent();
-                        if (!((response.status === 200 && position === 0) ||
-                            response.status === 206)) return [3 /*break*/, 3];
-                        _b = (_a = Buffer).from;
-                        return [4 /*yield*/, response.arrayBuffer()];
-                    case 2:
-                        nodeBuffer = _b.apply(_a, [_c.sent()]);
-                        sizeMatch = /\/(\d+)$/.exec(response.headers.get('content-range'));
-                        if (sizeMatch[1]) {
-                            this._stat = { size: parseInt(sizeMatch[1], 10) };
-                        }
-                        return [2 /*return*/, nodeBuffer];
-                    case 3: throw new Error("HTTP ".concat(response.status, " fetching ").concat(this.url));
-                }
-            });
-        });
-    };
-    RemoteFile.prototype.read = function (buffer, offset, length, position) {
-        if (offset === void 0) { offset = 0; }
-        if (length === void 0) { length = Infinity; }
-        if (position === void 0) { position = 0; }
-        var readPosition = position;
-        if (readPosition === null) {
-            readPosition = this.position;
-            this.position += length;
-        }
-        return this.cache.get(buffer, offset, length, position);
-    };
-    RemoteFile.prototype.readFile = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var response, _a, _b;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
-                    case 0: return [4 /*yield*/, (0, cross_fetch_1.default)(this.url, {
-                            method: 'GET',
-                            redirect: 'follow',
-                            mode: 'cors',
-                        })];
-                    case 1:
-                        response = _c.sent();
-                        _b = (_a = Buffer).from;
-                        return [4 /*yield*/, response.arrayBuffer()];
-                    case 2: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
-                }
-            });
-        });
-    };
-    RemoteFile.prototype.stat = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var buf;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        if (!!this._stat) return [3 /*break*/, 2];
-                        buf = Buffer.allocUnsafe(10);
-                        return [4 /*yield*/, this.read(buf, 0, 10, 0)];
-                    case 1:
-                        _a.sent();
-                        if (!this._stat) {
-                            throw new Error("unable to determine size of file at ".concat(this.url));
-                        }
-                        _a.label = 2;
-                    case 2: return [2 /*return*/, this._stat];
-                }
-            });
-        });
-    };
-    return RemoteFile;
-}());
-exports.default = RemoteFile;
-//# sourceMappingURL=remoteFile.js.map

package/dist/io/remoteFile.js.map

@@ -1 +0,0 @@
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package/esm/io/bufferCache.d.ts

@@ -1,12 +0,0 @@
-export default class BufferCache {
-    constructor({ fetch, size, chunkSize }: {
-        fetch: any;
-        size?: number | undefined;
-        chunkSize?: number | undefined;
-    });
-    fetch: any;
-    chunkSize: number;
-    lruCache: any;
-    get(outputBuffer: any, offset: any, length: any, position: any): Promise<void>;
-    _getChunk(chunkNumber: any): any;
-}

package/esm/io/bufferCache.js

@@ -1,54 +0,0 @@
-import LRU from 'quick-lru';
-export default class BufferCache {
-    constructor({ fetch, size = 10000000, chunkSize = 32768 }) {
-        if (!fetch) {
-            throw new Error('fetch function required');
-        }
-        this.fetch = fetch;
-        this.chunkSize = chunkSize;
-        this.lruCache = new LRU({ maxSize: Math.floor(size / chunkSize) });
-    }
-    async get(outputBuffer, offset, length, position) {
-        if (outputBuffer.length < offset + length) {
-            throw new Error('output buffer not big enough for request');
-        }
-        // calculate the list of chunks involved in this fetch
-        const firstChunk = Math.floor(position / this.chunkSize);
-        const lastChunk = Math.floor((position + length) / this.chunkSize);
-        // fetch them all as necessary
-        const fetches = new Array(lastChunk - firstChunk + 1);
-        for (let chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
-            fetches[chunk - firstChunk] = this._getChunk(chunk).then(data => ({
-                data,
-                chunkNumber: chunk,
-            }));
-        }
-        // stitch together the response buffer using them
-        const chunks = await Promise.all(fetches);
-        const chunksOffset = position - chunks[0].chunkNumber * this.chunkSize;
-        chunks.forEach(({ data, chunkNumber }) => {
-            const chunkPositionStart = chunkNumber * this.chunkSize;
-            let copyStart = 0;
-            let copyEnd = this.chunkSize;
-            let copyOffset = offset + (chunkNumber - firstChunk) * this.chunkSize - chunksOffset;
-            if (chunkNumber === firstChunk) {
-                copyOffset = offset;
-                copyStart = chunksOffset;
-            }
-            if (chunkNumber === lastChunk) {
-                copyEnd = position + length - chunkPositionStart;
-            }
-            data.copy(outputBuffer, copyOffset, copyStart, copyEnd);
-        });
-    }
-    _getChunk(chunkNumber) {
-        const cachedPromise = this.lruCache.get(chunkNumber);
-        if (cachedPromise) {
-            return cachedPromise;
-        }
-        const freshPromise = this.fetch(chunkNumber * this.chunkSize, this.chunkSize);
-        this.lruCache.set(chunkNumber, freshPromise);
-        return freshPromise;
-    }
-}
-//# sourceMappingURL=bufferCache.js.map

package/esm/io/bufferCache.js.map

@@ -1 +0,0 @@
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package/esm/io/localFile.d.ts

@@ -1,10 +0,0 @@
-export default class LocalFile {
-    constructor(source: any);
-    position: number;
-    filename: any;
-    fd: any;
-    read(buffer: any, offset: number | undefined, length: any, position: any): Promise<any>;
-    readFile(): Promise<any>;
-    stat(): Promise<any>;
-    _stat: any;
-}

package/esm/io/localFile.js

@@ -1,31 +0,0 @@
-import { promisify } from 'es6-promisify';
-import fs from 'fs';
-const fsOpen = fs && promisify(fs.open);
-const fsRead = fs && promisify(fs.read);
-const fsFStat = fs && promisify(fs.fstat);
-const fsReadFile = fs && promisify(fs.readFile);
-export default class LocalFile {
-    constructor(source) {
-        this.position = 0;
-        this.filename = source;
-        this.fd = fsOpen(this.filename, 'r');
-    }
-    async read(buffer, offset = 0, length, position) {
-        let readPosition = position;
-        if (readPosition === null) {
-            readPosition = this.position;
-            this.position += length;
-        }
-        return fsRead(await this.fd, buffer, offset, length, position);
-    }
-    async readFile() {
-        return fsReadFile(await this.fd);
-    }
-    async stat() {
-        if (!this._stat) {
-            this._stat = await fsFStat(await this.fd);
-        }
-        return this._stat;
-    }
-}
-//# sourceMappingURL=localFile.js.map

package/esm/io/localFile.js.map

@@ -1 +0,0 @@
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package/esm/io/remoteFile.d.ts

@@ -1,16 +0,0 @@
-export default class RemoteFile {
-    constructor(source: any);
-    position: number;
-    url: any;
-    cache: BufferCache;
-    _fetch(position: any, length: any): Promise<Buffer>;
-    _stat: {
-        size: number;
-    } | undefined;
-    read(buffer: any, offset?: number, length?: number, position?: number): Promise<void>;
-    readFile(): Promise<Buffer>;
-    stat(): Promise<{
-        size: number;
-    }>;
-}
-import BufferCache from "./bufferCache";

package/esm/io/remoteFile.js

@@ -1,64 +0,0 @@
-import fetch from 'cross-fetch';
-import BufferCache from './bufferCache';
-export default class RemoteFile {
-    constructor(source) {
-        this.position = 0;
-        this.url = source;
-        this.cache = new BufferCache({
-            fetch: (start, length) => this._fetch(start, length),
-        });
-    }
-    async _fetch(position, length) {
-        const headers = {};
-        if (length < Infinity) {
-            headers.range = `bytes=${position}-${position + length}`;
-        }
-        else if (length === Infinity && position !== 0) {
-            headers.range = `bytes=${position}-`;
-        }
-        const response = await fetch(this.url, {
-            method: 'GET',
-            headers,
-            redirect: 'follow',
-            mode: 'cors',
-        });
-        if ((response.status === 200 && position === 0) ||
-            response.status === 206) {
-            const nodeBuffer = Buffer.from(await response.arrayBuffer());
-            // try to parse out the size of the remote file
-            const sizeMatch = /\/(\d+)$/.exec(response.headers.get('content-range'));
-            if (sizeMatch[1]) {
-                this._stat = { size: parseInt(sizeMatch[1], 10) };
-            }
-            return nodeBuffer;
-        }
-        throw new Error(`HTTP ${response.status} fetching ${this.url}`);
-    }
-    read(buffer, offset = 0, length = Infinity, position = 0) {
-        let readPosition = position;
-        if (readPosition === null) {
-            readPosition = this.position;
-            this.position += length;
-        }
-        return this.cache.get(buffer, offset, length, position);
-    }
-    async readFile() {
-        const response = await fetch(this.url, {
-            method: 'GET',
-            redirect: 'follow',
-            mode: 'cors',
-        });
-        return Buffer.from(await response.arrayBuffer());
-    }
-    async stat() {
-        if (!this._stat) {
-            const buf = Buffer.allocUnsafe(10);
-            await this.read(buf, 0, 10, 0);
-            if (!this._stat) {
-                throw new Error(`unable to determine size of file at ${this.url}`);
-            }
-        }
-        return this._stat;
-    }
-}
-//# sourceMappingURL=remoteFile.js.map

package/esm/io/remoteFile.js.map

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package/src/cramFile/codecs/_base.js

@@ -1,49 +0,0 @@
-import { CramBufferOverrunError } from '../../errors'
-
-const validDataTypes = {
-  int: true,
-  byte: true,
-  long: true,
-  byteArray: true,
-  byteArrayBlock: true,
-}
-
-// codec base class
-export default class CramCodec {
-  constructor(parameters = {}, dataType) {
-    this.parameters = parameters
-    this.dataType = dataType
-    if (!dataType) {
-      throw new TypeError('must provide a data type to codec constructor')
-    }
-    if (!validDataTypes[dataType]) {
-      throw new TypeError(`invalid data type ${dataType}`)
-    }
-  }
-
-  // decode(slice, coreDataBlock, blocksByContentId, cursors) {
-  // }
-
-  _getBits(data, cursor, numBits) {
-    let val = 0
-    if (
-      cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >
-      data.length
-    ) {
-      throw new CramBufferOverrunError(
-        'read error during decoding. the file seems to be truncated.',
-      )
-    }
-    for (let dlen = numBits; dlen; dlen -= 1) {
-      // get the next `dlen` bits in the input, put them in val
-      val <<= 1
-      val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1
-      cursor.bitPosition -= 1
-      if (cursor.bitPosition < 0) {
-        cursor.bytePosition += 1
-      }
-      cursor.bitPosition &= 7
-    }
-    return val
-  }
-}

package/src/cramFile/codecs/beta.js

@@ -1,23 +0,0 @@
-import { CramUnimplementedError } from '../../errors'
-import CramCodec from './_base'
-
-export default class BetaCodec extends CramCodec {
-  constructor(parameters = {}, dataType) {
-    super(parameters, dataType)
-    if (this.dataType !== 'int') {
-      throw new CramUnimplementedError(
-        `${this.dataType} decoding not yet implemented by BETA codec`,
-      )
-    }
-  }
-
-  decode(slice, coreDataBlock, blocksByContentId, cursors) {
-    const data =
-      this._getBits(
-        coreDataBlock.content,
-        cursors.coreBlock,
-        this.parameters.length,
-      ) - this.parameters.offset
-    return data
-  }
-}

package/src/cramFile/codecs/gamma.js

@@ -1,30 +0,0 @@
-import { CramUnimplementedError } from '../../errors'
-import CramCodec from './_base'
-
-export default class GammaCodec extends CramCodec {
-  constructor(parameters = {}, dataType) {
-    super(parameters, dataType)
-    if (this.dataType !== 'int') {
-      throw new CramUnimplementedError(
-        `${this.dataType} decoding not yet implemented by GAMMA codec`,
-      )
-    }
-  }
-
-  decode(slice, coreDataBlock, blocksByContentId, cursors) {
-    let length = 1
-
-    while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
-      length += 1
-    }
-
-    const readBits = this._getBits(
-      coreDataBlock.content,
-      cursors.coreBlock,
-      length - 1,
-    )
-
-    const value = readBits | (1 << (length - 1))
-    return value - this.parameters.offset
-  }
-}

package/src/cramFile/codecs/subexp.js

@@ -1,32 +0,0 @@
-import { CramUnimplementedError } from '../../errors'
-import CramCodec from './_base'
-
-export default class SubexpCodec extends CramCodec {
-  constructor(parameters = {}, dataType) {
-    super(parameters, dataType)
-    if (this.dataType !== 'int') {
-      throw new CramUnimplementedError(
-        `${this.dataType} decoding not yet implemented by SUBEXP codec`,
-      )
-    }
-  }
-
-  decode(slice, coreDataBlock, blocksByContentId, cursors) {
-    let numLeadingOnes = 0
-    while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
-      numLeadingOnes += 1
-    }
-
-    let b
-    let n
-    if (numLeadingOnes === 0) {
-      b = this.parameters.K
-      n = this._getBits(coreDataBlock.content, cursors.coreBlock, b)
-    } else {
-      b = numLeadingOnes + this.parameters.K - 1
-      n = (1 << b) | this._getBits(coreDataBlock.content, cursors.coreBlock, b)
-    }
-
-    return n - this.parameters.offset
-  }
-}

package/src/io/bufferCache.js

@@ -1,66 +0,0 @@
-import LRU from 'quick-lru'
-
-export default class BufferCache {
-  constructor({ fetch, size = 10000000, chunkSize = 32768 }) {
-    if (!fetch) {
-      throw new Error('fetch function required')
-    }
-    this.fetch = fetch
-    this.chunkSize = chunkSize
-    this.lruCache = new LRU({ maxSize: Math.floor(size / chunkSize) })
-  }
-
-  async get(outputBuffer, offset, length, position) {
-    if (outputBuffer.length < offset + length) {
-      throw new Error('output buffer not big enough for request')
-    }
-
-    // calculate the list of chunks involved in this fetch
-    const firstChunk = Math.floor(position / this.chunkSize)
-    const lastChunk = Math.floor((position + length) / this.chunkSize)
-
-    // fetch them all as necessary
-    const fetches = new Array(lastChunk - firstChunk + 1)
-    for (let chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
-      fetches[chunk - firstChunk] = this._getChunk(chunk).then(data => ({
-        data,
-        chunkNumber: chunk,
-      }))
-    }
-
-    // stitch together the response buffer using them
-    const chunks = await Promise.all(fetches)
-    const chunksOffset = position - chunks[0].chunkNumber * this.chunkSize
-    chunks.forEach(({ data, chunkNumber }) => {
-      const chunkPositionStart = chunkNumber * this.chunkSize
-      let copyStart = 0
-      let copyEnd = this.chunkSize
-      let copyOffset =
-        offset + (chunkNumber - firstChunk) * this.chunkSize - chunksOffset
-
-      if (chunkNumber === firstChunk) {
-        copyOffset = offset
-        copyStart = chunksOffset
-      }
-      if (chunkNumber === lastChunk) {
-        copyEnd = position + length - chunkPositionStart
-      }
-
-      data.copy(outputBuffer, copyOffset, copyStart, copyEnd)
-    })
-  }
-
-  _getChunk(chunkNumber) {
-    const cachedPromise = this.lruCache.get(chunkNumber)
-    if (cachedPromise) {
-      return cachedPromise
-    }
-
-    const freshPromise = this.fetch(
-      chunkNumber * this.chunkSize,
-      this.chunkSize,
-    )
-    this.lruCache.set(chunkNumber, freshPromise)
-    return freshPromise
-  }
-}

package/src/io/localFile.js

@@ -1,35 +0,0 @@
-import { promisify } from 'es6-promisify'
-import fs from 'fs'
-
-const fsOpen = fs && promisify(fs.open)
-const fsRead = fs && promisify(fs.read)
-const fsFStat = fs && promisify(fs.fstat)
-const fsReadFile = fs && promisify(fs.readFile)
-
-export default class LocalFile {
-  constructor(source) {
-    this.position = 0
-    this.filename = source
-    this.fd = fsOpen(this.filename, 'r')
-  }
-
-  async read(buffer, offset = 0, length, position) {
-    let readPosition = position
-    if (readPosition === null) {
-      readPosition = this.position
-      this.position += length
-    }
-    return fsRead(await this.fd, buffer, offset, length, position)
-  }
-
-  async readFile() {
-    return fsReadFile(await this.fd)
-  }
-
-  async stat() {
-    if (!this._stat) {
-      this._stat = await fsFStat(await this.fd)
-    }
-    return this._stat
-  }
-}

package/src/io/remoteFile.js

@@ -1,71 +0,0 @@
-import fetch from 'cross-fetch'
-import BufferCache from './bufferCache'
-
-export default class RemoteFile {
-  constructor(source) {
-    this.position = 0
-    this.url = source
-    this.cache = new BufferCache({
-      fetch: (start, length) => this._fetch(start, length),
-    })
-  }
-
-  async _fetch(position, length) {
-    const headers = {}
-    if (length < Infinity) {
-      headers.range = `bytes=${position}-${position + length}`
-    } else if (length === Infinity && position !== 0) {
-      headers.range = `bytes=${position}-`
-    }
-    const response = await fetch(this.url, {
-      method: 'GET',
-      headers,
-      redirect: 'follow',
-      mode: 'cors',
-    })
-    if (
-      (response.status === 200 && position === 0) ||
-      response.status === 206
-    ) {
-      const nodeBuffer = Buffer.from(await response.arrayBuffer())
-
-      // try to parse out the size of the remote file
-      const sizeMatch = /\/(\d+)$/.exec(response.headers.get('content-range'))
-      if (sizeMatch[1]) {
-        this._stat = { size: parseInt(sizeMatch[1], 10) }
-      }
-
-      return nodeBuffer
-    }
-    throw new Error(`HTTP ${response.status} fetching ${this.url}`)
-  }
-
-  read(buffer, offset = 0, length = Infinity, position = 0) {
-    let readPosition = position
-    if (readPosition === null) {
-      readPosition = this.position
-      this.position += length
-    }
-    return this.cache.get(buffer, offset, length, position)
-  }
-
-  async readFile() {
-    const response = await fetch(this.url, {
-      method: 'GET',
-      redirect: 'follow',
-      mode: 'cors',
-    })
-    return Buffer.from(await response.arrayBuffer())
-  }
-
-  async stat() {
-    if (!this._stat) {
-      const buf = Buffer.allocUnsafe(10)
-      await this.read(buf, 0, 10, 0)
-      if (!this._stat) {
-        throw new Error(`unable to determine size of file at ${this.url}`)
-      }
-    }
-    return this._stat
-  }
-}