@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/container/index.js

@@ -1,290 +1,176 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _assign = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/assign"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _context7;
-
-var _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var _require2 = require('../util'),
-    itf8Size = _require2.itf8Size,
-    parseItem = _require2.parseItem,
-    tinyMemoize = _require2.tinyMemoize;
-
-var CramSlice = require('../slice');
-
-var CramContainerCompressionScheme = require('./compressionScheme');
-
-var CramContainer =
-/*#__PURE__*/
-function () {
-  function CramContainer(cramFile, position) {
-    (0, _classCallCheck2.default)(this, CramContainer);
-    // cram file this container comes from
-    this.file = cramFile; // position of this container in the file
-
-    this.filePosition = position; // console.log(`container: ${this.filePosition}`)
-  } // memoize
-
-
-  (0, _createClass2.default)(CramContainer, [{
-    key: "getHeader",
-    value: function getHeader() {
-      return this._readContainerHeader(this.filePosition);
-    } // memoize
-
-  }, {
-    key: "getCompressionHeaderBlock",
-    value: function () {
-      var _getCompressionHeaderBlock = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee() {
-        var containerHeader, sectionParsers, block, content;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.getHeader();
-
-              case 2:
-                containerHeader = _context.sent;
-
-                if (containerHeader.numRecords) {
-                  _context.next = 5;
-                  break;
-                }
-
-                return _context.abrupt("return", null);
-
-              case 5:
-                _context.next = 7;
-                return this.file.getSectionParsers();
-
-              case 7:
-                sectionParsers = _context.sent;
-                _context.next = 10;
-                return this.getFirstBlock();
-
-              case 10:
-                block = _context.sent;
-
-                if (!(block.contentType !== 'COMPRESSION_HEADER')) {
-                  _context.next = 13;
-                  break;
-                }
-
-                throw new CramMalformedError("invalid content type ".concat(block.contentType, " in what is supposed to be the compression header block"));
-
-              case 13:
-                content = parseItem(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
-                block.content = content;
-                return _context.abrupt("return", block);
-
-              case 16:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getCompressionHeaderBlock() {
-        return _getCompressionHeaderBlock.apply(this, arguments);
-      }
-
-      return getCompressionHeaderBlock;
-    }()
-  }, {
-    key: "getFirstBlock",
-    value: function () {
-      var _getFirstBlock = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2() {
-        var containerHeader;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.getHeader();
-
-              case 2:
-                containerHeader = _context2.sent;
-                return _context2.abrupt("return", this.file.readBlock(containerHeader._endPosition));
-
-              case 4:
-              case "end":
-                return _context2.stop();
+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;
             }
-          }
-        }, _callee2, this);
-      }));
-
-      function getFirstBlock() {
-        return _getFirstBlock.apply(this, arguments);
-      }
-
-      return getFirstBlock;
-    }() // parses the compression header data into a CramContainerCompressionScheme object
+            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 errors_1 = require("../../errors");
+var util_1 = require("../util");
+var slice_1 = __importDefault(require("../slice"));
+var compressionScheme_1 = __importDefault(require("./compressionScheme"));
+var CramContainer = /** @class */ (function () {
+    function CramContainer(cramFile, position) {
+        // cram file this container comes from
+        this.file = cramFile;
+        // position of this container in the file
+        this.filePosition = position;
+        // console.log(`container: ${this.filePosition}`)
+    }
     // memoize
-
-  }, {
-    key: "getCompressionScheme",
-    value: function () {
-      var _getCompressionScheme = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee3() {
-        var header;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.getCompressionHeaderBlock();
-
-              case 2:
-                header = _context3.sent;
-
-                if (header) {
-                  _context3.next = 5;
-                  break;
+    CramContainer.prototype.getHeader = function () {
+        return this._readContainerHeader(this.filePosition);
+    };
+    // memoize
+    CramContainer.prototype.getCompressionHeaderBlock = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var containerHeader, sectionParsers, block, content;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()
+                        // if there are no records in the container, there will be no compression header
+                    ];
+                    case 1:
+                        containerHeader = _a.sent();
+                        // if there are no records in the container, there will be no compression header
+                        if (!containerHeader.numRecords) {
+                            return [2 /*return*/, null];
+                        }
+                        return [4 /*yield*/, this.file.getSectionParsers()];
+                    case 2:
+                        sectionParsers = _a.sent();
+                        return [4 /*yield*/, this.getFirstBlock()];
+                    case 3:
+                        block = _a.sent();
+                        if (block.contentType !== 'COMPRESSION_HEADER') {
+                            throw new errors_1.CramMalformedError("invalid content type ".concat(block.contentType, " in what is supposed to be the compression header block"));
+                        }
+                        content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
+                        block.content = content;
+                        return [2 /*return*/, block];
                 }
-
-                return _context3.abrupt("return", undefined);
-
-              case 5:
-                return _context3.abrupt("return", new CramContainerCompressionScheme(header.content));
-
-              case 6:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getCompressionScheme() {
-        return _getCompressionScheme.apply(this, arguments);
-      }
-
-      return getCompressionScheme;
-    }()
-  }, {
-    key: "getSlice",
-    value: function getSlice(slicePosition, sliceSize) {
-      // note: slicePosition is relative to the end of the container header
-      // TODO: perhaps we should cache slices?
-      return new CramSlice(this, slicePosition, sliceSize);
-    }
-  }, {
-    key: "_readContainerHeader",
-    value: function () {
-      var _readContainerHeader2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee4(position) {
-        var sectionParsers, cramContainerHeader1, cramContainerHeader2, _ref, fileSize, bytes1, header1, numLandmarksSize, _context4, _context5, bytes2, header2, completeHeader;
-
-        return _regenerator.default.wrap(function _callee4$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                _context6.next = 2;
-                return this.file.getSectionParsers();
-
-              case 2:
-                sectionParsers = _context6.sent;
-                cramContainerHeader1 = sectionParsers.cramContainerHeader1, cramContainerHeader2 = sectionParsers.cramContainerHeader2;
-                _context6.next = 6;
-                return this.file.stat();
-
-              case 6:
-                _ref = _context6.sent;
-                fileSize = _ref.size;
-
-                if (!(position >= fileSize)) {
-                  _context6.next = 10;
-                  break;
+            });
+        });
+    };
+    CramContainer.prototype.getFirstBlock = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var containerHeader;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()];
+                    case 1:
+                        containerHeader = _a.sent();
+                        return [2 /*return*/, this.file.readBlock(containerHeader._endPosition)];
                 }
-
-                return _context6.abrupt("return", undefined);
-
-              case 10:
-                // parse the container header. do it in 2 pieces because you cannot tell
-                // how much to buffer until you read numLandmarks
-                bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
-                _context6.next = 13;
-                return this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
-
-              case 13:
-                header1 = parseItem(bytes1, cramContainerHeader1.parser);
-                numLandmarksSize = itf8Size(header1.numLandmarks);
-
-                if (!(position + header1.length >= fileSize)) {
-                  _context6.next = 18;
-                  break;
+            });
+        });
+    };
+    // parses the compression header data into a CramContainerCompressionScheme object
+    // memoize
+    CramContainer.prototype.getCompressionScheme = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getCompressionHeaderBlock()];
+                    case 1:
+                        header = _a.sent();
+                        if (!header) {
+                            return [2 /*return*/, undefined];
+                        }
+                        return [2 /*return*/, new compressionScheme_1.default(header.content)];
                 }
-
-                console.warn((0, _concat.default)(_context4 = (0, _concat.default)(_context5 = "".concat(this.file, ": container header at ")).call(_context5, position, " indicates that the container has length ")).call(_context4, header1.length, ", which extends beyond the length of the file. Skipping this container."));
-                return _context6.abrupt("return", undefined);
-
-              case 18:
-                bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
-                _context6.next = 21;
-                return this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
-
-              case 21:
-                header2 = parseItem(bytes2, cramContainerHeader2.parser);
-
-                if (!(this.file.validateChecksums && header2.crc32 !== undefined)) {
-                  _context6.next = 25;
-                  break;
+            });
+        });
+    };
+    CramContainer.prototype.getSlice = function (slicePosition, sliceSize) {
+        // note: slicePosition is relative to the end of the container header
+        // TODO: perhaps we should cache slices?
+        return new slice_1.default(this, slicePosition, sliceSize);
+    };
+    CramContainer.prototype._readContainerHeader = function (position) {
+        return __awaiter(this, void 0, void 0, function () {
+            var sectionParsers, cramContainerHeader1, cramContainerHeader2, fileSize, bytes1, header1, numLandmarksSize, bytes2, header2, completeHeader;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.file.getSectionParsers()];
+                    case 1:
+                        sectionParsers = _a.sent();
+                        cramContainerHeader1 = sectionParsers.cramContainerHeader1, cramContainerHeader2 = sectionParsers.cramContainerHeader2;
+                        return [4 /*yield*/, this.file.stat()];
+                    case 2:
+                        fileSize = (_a.sent()).size;
+                        if (position >= fileSize) {
+                            return [2 /*return*/, undefined];
+                        }
+                        bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
+                        return [4 /*yield*/, this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position)];
+                    case 3:
+                        _a.sent();
+                        header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
+                        numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
+                        if (position + header1.length >= fileSize) {
+                            console.warn("".concat(this.file, ": container header at ").concat(position, " indicates that the container has length ").concat(header1.length, ", which extends beyond the length of the file. Skipping this container."));
+                            return [2 /*return*/, undefined];
+                        }
+                        bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
+                        return [4 /*yield*/, this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize)];
+                    case 4:
+                        _a.sent();
+                        header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
+                        if (!(this.file.validateChecksums && header2.crc32 !== undefined)) return [3 /*break*/, 6];
+                        return [4 /*yield*/, this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, "container header beginning at position ".concat(position))];
+                    case 5:
+                        _a.sent();
+                        _a.label = 6;
+                    case 6:
+                        completeHeader = Object.assign(header1, header2, {
+                            _size: header1._size + header2._size - numLandmarksSize,
+                            _endPosition: header1._size + header2._size - numLandmarksSize + position,
+                        });
+                        return [2 /*return*/, completeHeader];
                 }
-
-                _context6.next = 25;
-                return this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, "container header beginning at position ".concat(position));
-
-              case 25:
-                completeHeader = (0, _assign.default)(header1, header2, {
-                  _size: header1._size + header2._size - numLandmarksSize,
-                  _endPosition: header1._size + header2._size - numLandmarksSize + position
-                });
-                return _context6.abrupt("return", completeHeader);
-
-              case 27:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function _readContainerHeader(_x) {
-        return _readContainerHeader2.apply(this, arguments);
-      }
-
-      return _readContainerHeader;
-    }()
-  }]);
-  return CramContainer;
-}();
-
-(0, _forEach.default)(_context7 = 'getHeader getCompressionHeaderBlock getCompressionScheme'.split(' ')).call(_context7, function (method) {
-  return tinyMemoize(CramContainer, method);
-});
-module.exports = CramContainer;
+            });
+        });
+    };
+    return CramContainer;
+}());
+exports.default = CramContainer;
+'getHeader getCompressionHeaderBlock getCompressionScheme'
+    .split(' ')
+    .forEach(function (method) { return (0, util_1.tinyMemoize)(CramContainer, method); });
+//# sourceMappingURL=index.js.map

package/dist/cramFile/container/index.js.map

@@ -0,0 +1 @@
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package/dist/cramFile/file.d.ts

@@ -0,0 +1,63 @@
+export default class CramFile {
+    /**
+     * @param {object} args
+     * @param {object} [args.filehandle] - a filehandle that implements the stat() and
+     * read() methods of the Node filehandle API https://nodejs.org/api/fs.html#fs_class_filehandle
+     * @param {object} [args.path] - path to the cram file
+     * @param {object} [args.url] - url for the cram file.  also supports file:// urls for local files
+     * @param {function} [args.seqFetch] - a function with signature
+     * `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
+     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
+     * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
+     */
+    constructor(args: {
+        filehandle?: object | undefined;
+        path?: object | undefined;
+        url?: object | undefined;
+        seqFetch?: Function | undefined;
+        cacheSize?: number | undefined;
+        checkSequenceMD5?: boolean | undefined;
+    });
+    file: any;
+    validateChecksums: boolean;
+    fetchReferenceSequenceCallback: Function | undefined;
+    options: {
+        checkSequenceMD5: boolean;
+        cacheSize: number;
+    };
+    featureCache: any;
+    toString(): any;
+    read(buffer: any, offset: any, length: any, position: any): any;
+    stat(): any;
+    getDefinition(): Promise<any>;
+    getSamHeader(): Promise<any[]>;
+    header: any;
+    getHeaderText(): Promise<any>;
+    getSectionParsers(): Promise<{
+        cramFileDefinition: {
+            parser: any;
+            maxLength: number;
+        };
+        cramBlockHeader: {
+            parser: any;
+            maxLength: number;
+        };
+        cramBlockCrc32: {
+            parser: any;
+            maxLength: number;
+        };
+    }>;
+    getContainerById(containerNumber: any): Promise<CramContainer | undefined>;
+    checkCrc32(position: any, length: any, recordedCrc32: any, description: any): Promise<void>;
+    /**
+     * @returns {Promise[number]} the number of containers in the file
+     */
+    containerCount(): any;
+    getContainerAtPosition(position: any): CramContainer;
+    readBlockHeader(position: any): Promise<any>;
+    _parseSection(section: any, position: any, size: any, preReadBuffer: any): Promise<any>;
+    _uncompress(compressionMethod: any, inputBuffer: any, outputBuffer: any): void;
+    readBlock(position: any): Promise<any>;
+}
+import CramContainer from "./container";