@gmod/bam 1.1.8 → 1.1.9

package/dist/htsget.js.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -1,55 +1,17 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _Object$defineProperty = require("@babel/runtime-corejs3/core-js-stable/object/define-property");
-
-_Object$defineProperty(exports, "__esModule", {
-  value: true
-});
-
-_Object$defineProperty(exports, "BAI", {
-  enumerable: true,
-  get: function get() {
-    return _bai.default;
-  }
-});
-
-_Object$defineProperty(exports, "CSI", {
-  enumerable: true,
-  get: function get() {
-    return _csi.default;
-  }
-});
-
-_Object$defineProperty(exports, "BamFile", {
-  enumerable: true,
-  get: function get() {
-    return _bamFile.default;
-  }
-});
-
-_Object$defineProperty(exports, "HtsgetFile", {
-  enumerable: true,
-  get: function get() {
-    return _htsget.default;
-  }
-});
-
-_Object$defineProperty(exports, "BamRecord", {
-  enumerable: true,
-  get: function get() {
-    return _record.default;
-  }
-});
-
-var _bai = _interopRequireDefault(require("./bai"));
-
-var _csi = _interopRequireDefault(require("./csi"));
-
-var _bamFile = _interopRequireDefault(require("./bamFile"));
-
-var _htsget = _interopRequireDefault(require("./htsget"));
-
-var _record = _interopRequireDefault(require("./record"));
-//# sourceMappingURL=data:application/json;charset=utf-8;base64,eyJ2ZXJzaW9uIjozLCJzb3VyY2VzIjpbIi4uL3NyYy9pbmRleC50cyJdLCJuYW1lcyI6W10sIm1hcHBpbmdzIjoiOzs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7QUFBQTs7QUFDQTs7QUFDQTs7QUFDQTs7QUFDQSIsInNvdXJjZXNDb250ZW50IjpbImltcG9ydCBCQUkgZnJvbSAnLi9iYWknXG5pbXBvcnQgQ1NJIGZyb20gJy4vY3NpJ1xuaW1wb3J0IEJhbUZpbGUgZnJvbSAnLi9iYW1GaWxlJ1xuaW1wb3J0IEh0c2dldEZpbGUgZnJvbSAnLi9odHNnZXQnXG5pbXBvcnQgQmFtUmVjb3JkIGZyb20gJy4vcmVjb3JkJ1xuXG5leHBvcnQgeyBCQUksIENTSSwgQmFtRmlsZSwgQmFtUmVjb3JkLCBIdHNnZXRGaWxlIH1cbiJdfQ==
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.HtsgetFile = exports.BamRecord = exports.BamFile = exports.CSI = exports.BAI = void 0;
+var bai_1 = __importDefault(require("./bai"));
+exports.BAI = bai_1.default;
+var csi_1 = __importDefault(require("./csi"));
+exports.CSI = csi_1.default;
+var bamFile_1 = __importDefault(require("./bamFile"));
+exports.BamFile = bamFile_1.default;
+var htsget_1 = __importDefault(require("./htsget"));
+exports.HtsgetFile = htsget_1.default;
+var record_1 = __importDefault(require("./record"));
+exports.BamRecord = record_1.default;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAuB;AAMd,cANF,aAAG,CAME;AALZ,8CAAuB;AAKT,cALP,aAAG,CAKO;AAJjB,sDAA+B;AAIZ,kBAJZ,iBAAO,CAIY;AAH1B,oDAAiC;AAGM,qBAHhC,gBAAU,CAGgC;AAFjD,oDAAgC;AAEJ,oBAFrB,gBAAS,CAEqB"}

package/dist/indexFile.d.ts

@@ -4,8 +4,7 @@ import Chunk from './chunk';
 import { BaseOpts } from './util';
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
-    renameRefSeq: Function;
-    private _parseCache;
+    renameRefSeq: (s: string) => string;
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]

package/dist/indexFile.js

@@ -1,167 +1,81 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _Object$defineProperty2 = require("@babel/runtime-corejs3/core-js-stable/object/define-property");
-
-_Object$defineProperty2(exports, "__esModule", {
-  value: true
-});
-
-exports.default = void 0;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/define-property"));
-
-var _defineProperties = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/define-properties"));
-
-var _getOwnPropertyDescriptors = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/get-own-property-descriptors"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _getOwnPropertyDescriptor = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/get-own-property-descriptor"));
-
-var _filter = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/filter"));
-
-var _getOwnPropertySymbols = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/get-own-property-symbols"));
-
-var _keys = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/keys"));
-
-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 _defineProperty3 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/defineProperty"));
-
-var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
-
-var _quickLru = _interopRequireDefault(require("quick-lru"));
-
-function ownKeys(object, enumerableOnly) { var keys = (0, _keys.default)(object); if (_getOwnPropertySymbols.default) { var symbols = (0, _getOwnPropertySymbols.default)(object); if (enumerableOnly) symbols = (0, _filter.default)(symbols).call(symbols, function (sym) { return (0, _getOwnPropertyDescriptor.default)(object, sym).enumerable; }); keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { var _context3; (0, _forEach.default)(_context3 = ownKeys(Object(source), true)).call(_context3, function (key) { (0, _defineProperty3.default)(target, key, source[key]); }); } else if (_getOwnPropertyDescriptors.default) { (0, _defineProperties.default)(target, (0, _getOwnPropertyDescriptors.default)(source)); } else { var _context4; (0, _forEach.default)(_context4 = ownKeys(Object(source))).call(_context4, function (key) { (0, _defineProperty2.default)(target, key, (0, _getOwnPropertyDescriptor.default)(source, key)); }); } } return target; }
-
-var IndexFile = /*#__PURE__*/function () {
-  /**
-   * @param {filehandle} filehandle
-   * @param {function} [renameRefSeqs]
-   */
-  function IndexFile(_ref) {
-    var filehandle = _ref.filehandle,
-        _ref$renameRefSeq = _ref.renameRefSeq,
-        renameRefSeq = _ref$renameRefSeq === void 0 ? function (n) {
-      return n;
-    } : _ref$renameRefSeq;
-    (0, _classCallCheck2.default)(this, IndexFile);
-    (0, _defineProperty3.default)(this, "filehandle", void 0);
-    (0, _defineProperty3.default)(this, "renameRefSeq", void 0);
-    (0, _defineProperty3.default)(this, "_parseCache", void 0);
-    this.filehandle = filehandle;
-    this.renameRefSeq = renameRefSeq;
-  }
-
-  (0, _createClass2.default)(IndexFile, [{
-    key: "_findFirstData",
-    value: function _findFirstData(data, virtualOffset) {
-      var currentFdl = data.firstDataLine;
-
-      if (currentFdl) {
-        data.firstDataLine = currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
-      } else {
-        data.firstDataLine = virtualOffset;
-      }
-    }
-  }, {
-    key: "parse",
-    value: function () {
-      var _parse2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var _this = this;
-
-        var opts,
-            _args = arguments;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
-
-                if (!this._parseCache) {
-                  this._parseCache = new _abortablePromiseCache.default({
-                    cache: new _quickLru.default({
-                      maxSize: 1
-                    }),
-                    fill: function fill(opts, signal) {
-                      return _this._parse(_objectSpread(_objectSpread({}, opts), {}, {
-                        signal: signal
-                      }));
-                    }
-                  });
-                }
-
-                return _context.abrupt("return", this._parseCache.get('index', opts, opts.signal));
-
-              case 3:
-              case "end":
-                return _context.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;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function parse() {
-        return _parse2.apply(this, arguments);
-      }
-
-      return parse;
-    }()
-  }, {
-    key: "hasRefSeq",
-    value: function () {
-      var _hasRefSeq = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(seqId) {
-        var opts,
-            _args2 = arguments;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                opts = _args2.length > 1 && _args2[1] !== undefined ? _args2[1] : {};
-                _context2.next = 3;
-                return this.parse(opts);
-
-              case 3:
-                _context2.t1 = seqId;
-                _context2.t0 = _context2.sent.indices[_context2.t1];
-
-                if (_context2.t0) {
-                  _context2.next = 7;
-                  break;
+            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 };
+    }
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var IndexFile = /** @class */ (function () {
+    /**
+     * @param {filehandle} filehandle
+     * @param {function} [renameRefSeqs]
+     */
+    function IndexFile(_a) {
+        var filehandle = _a.filehandle, _b = _a.renameRefSeq, renameRefSeq = _b === void 0 ? function (n) { return n; } : _b;
+        this.filehandle = filehandle;
+        this.renameRefSeq = renameRefSeq;
+    }
+    IndexFile.prototype._findFirstData = function (data, virtualOffset) {
+        var currentFdl = data.firstDataLine;
+        if (currentFdl) {
+            data.firstDataLine =
+                currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
+        }
+        else {
+            data.firstDataLine = virtualOffset;
+        }
+    };
+    IndexFile.prototype.parse = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, this._parse(opts)];
+            });
+        });
+    };
+    IndexFile.prototype.hasRefSeq = function (seqId, opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.parse(opts)];
+                    case 1: return [2 /*return*/, !!((_a.sent()).indices[seqId] || {}).binIndex];
                 }
-
-                _context2.t0 = {};
-
-              case 7:
-                return _context2.abrupt("return", !!_context2.t0.binIndex);
-
-              case 8:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function hasRefSeq(_x) {
-        return _hasRefSeq.apply(this, arguments);
-      }
-
-      return hasRefSeq;
-    }()
-  }]);
-  return IndexFile;
-}();
-
+            });
+        });
+    };
+    return IndexFile;
+}());
 exports.default = IndexFile;
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+//# sourceMappingURL=indexFile.js.map

package/dist/indexFile.js.map

@@ -0,0 +1 @@
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