@gmod/tabix 1.5.0 → 1.5.3

package/dist/csi.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,yDAA6C;AAE7C,+DAA0D;AAC1D,kDAA2B;AAC3B,+BAAqD;AAErD,0DAAgD;AAEhD,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED;IAAiC,uBAAS;IAIxC,aAAY,IAAS;QAArB,YACE,kBAAM,IAAI,CAAC,SAIZ;QAHC,KAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,KAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,KAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;;IACnB,CAAC;IACK,uBAAS,GAAf,UAAgB,OAAe,EAAE,IAAkB;QAAlB,qBAAA,EAAA,SAAkB;;;;;4BAC/B,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAAlC,SAAS,GAAG,SAAsB;wBACxC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;wBACtC,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACpC,IAAI,CAAC,GAAG,EAAE;4BACR,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACO,KAAK,GAAK,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,MAA7B,CAA6B;wBAC1C,IAAI,KAAK,EAAE;4BACT,sBAAO,KAAK,CAAC,SAAS,EAAA;yBACvB;wBACD,sBAAO,CAAC,CAAC,EAAA;;;;KACV;IACK,sBAAQ,GAAd;;;gBACE,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;;;KAEvD;IAED,0BAAY,GAAZ,UAAa,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO;gBACL,WAAW,EAAE,EAAE;gBACf,WAAW,EAAE,EAAE;aAChB,CAAA;SACF;QAED,IAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,IAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,IAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,IAAI,KAAK,CAAC,4CAAqC,WAAW,CAAE,CAAC,CAAA;SACpE;QACD,IAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,IAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,IAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,IAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAElD,IAAA,KAA+B,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC1D,EAFO,WAAW,iBAAA,EAAE,WAAW,iBAE/B,CAAA;QAED,OAAO;YACL,WAAW,aAAA;YACX,WAAW,aAAA;YACX,SAAS,WAAA;YACT,QAAQ,UAAA;YACR,aAAa,eAAA;YACb,MAAM,QAAA;YACN,cAAc,gBAAA;SACf,CAAA;IACH,CAAC;IAED,6BAAe,GAAf,UAAgB,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,IAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,aAAA,EAAE,WAAW,aAAA,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IAEtB,oBAAM,GAAZ,UAAa,IAAkB;QAAlB,qBAAA,EAAA,SAAkB;;;;;;;wBACT,KAAA,uBAAK,CAAA;wBAAE,qBAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAA;4BAAjD,qBAAM,kBAAM,CAAC,SAAoC,CAAW,EAAC;wBAE3E,0BAA0B;sBAFiD;;wBAArE,KAAK,GAAG,SAA6D;wBAI3E,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BACxC,UAAU,GAAG,CAAC,CAAA;yBACf;6BAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BAC/C,UAAU,GAAG,CAAC,CAAA;yBACf;6BAAM;4BACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BACjC,oDAAoD;yBACrD;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBACrD,YAAY,GAAG,SAAA,CAAC,EAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA,CAAA;wBAEpD,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACnC,GAAG,GAGH;4BACF,WAAW,EAAE,EAAE;4BACf,WAAW,EAAE,EAAE;yBAChB,CAAA;wBACD,IAAI,SAAS,EAAE;4BACb,GAAG,GAAG,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAA;yBAC9C;wBACK,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;wBAI9C,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;wBAC7B,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;4BAC9C,oBAAoB;4BACpB,IAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;4BAC9C,UAAU,IAAI,CAAC,CAAA;4BACf,IAAM,QAAQ,GAA+B,EAAE,CAAA;4BAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;4BAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gCACpC,IAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gCAC1C,IAAI,GAAG,GAAG,KAAI,CAAC,YAAY,EAAE;oCAC3B,yDAAyD;oCACzD,qCAAqC;oCACrC,KAAK,GAAG,KAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oCAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,C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package/dist/index.js

@@ -1,37 +1,13 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");
-
-var _Object$defineProperty = require("@babel/runtime-corejs2/core-js/object/define-property");
-
-_Object$defineProperty(exports, "__esModule", {
-  value: true
-});
-
-_Object$defineProperty(exports, "TabixIndexedFile", {
-  enumerable: true,
-  get: function get() {
-    return _tabixIndexedFile.default;
-  }
-});
-
-_Object$defineProperty(exports, "TBI", {
-  enumerable: true,
-  get: function get() {
-    return _tbi.default;
-  }
-});
-
-_Object$defineProperty(exports, "CSI", {
-  enumerable: true,
-  get: function get() {
-    return _csi.default;
-  }
-});
-
-var _tabixIndexedFile = _interopRequireDefault(require("./tabixIndexedFile"));
-
-var _tbi = _interopRequireDefault(require("./tbi"));
-
-var _csi = _interopRequireDefault(require("./csi"));
-//# sourceMappingURL=data:application/json;charset=utf-8;base64,eyJ2ZXJzaW9uIjozLCJzb3VyY2VzIjpbIi4uL3NyYy9pbmRleC50cyJdLCJuYW1lcyI6W10sIm1hcHBpbmdzIjoiOzs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7Ozs7O0FBQUE7O0FBQ0E7O0FBQ0EiLCJzb3VyY2VzQ29udGVudCI6WyJpbXBvcnQgVGFiaXhJbmRleGVkRmlsZSBmcm9tICcuL3RhYml4SW5kZXhlZEZpbGUnXG5pbXBvcnQgVEJJIGZyb20gJy4vdGJpJ1xuaW1wb3J0IENTSSBmcm9tICcuL2NzaSdcblxuZXhwb3J0IHsgVGFiaXhJbmRleGVkRmlsZSwgVEJJLCBDU0kgfVxuIl19
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CSI = exports.TBI = exports.TabixIndexedFile = void 0;
+var tabixIndexedFile_1 = __importDefault(require("./tabixIndexedFile"));
+exports.TabixIndexedFile = tabixIndexedFile_1.default;
+var tbi_1 = __importDefault(require("./tbi"));
+exports.TBI = tbi_1.default;
+var csi_1 = __importDefault(require("./csi"));
+exports.CSI = csi_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,wEAAiD;AAIxC,2BAJF,0BAAgB,CAIE;AAHzB,8CAAuB;AAGI,cAHpB,aAAG,CAGoB;AAF9B,8CAAuB;AAES,cAFzB,aAAG,CAEyB"}

package/dist/indexFile.d.ts

@@ -7,7 +7,7 @@ export interface Options {
 }
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
-    renameRefSeq: Function;
+    renameRefSeq: (arg0: string) => string;
     private _parseCache;
     /**
      * @param {filehandle} filehandle

package/dist/indexFile.js

@@ -1,179 +1,118 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");
-
-var _Object$defineProperty = require("@babel/runtime-corejs2/core-js/object/define-property");
-
-_Object$defineProperty(exports, "__esModule", {
-  value: true
-});
-
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs2/regenerator"));
-
-var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/objectWithoutProperties"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/defineProperty"));
-
-var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
-
-var _quickLru = _interopRequireDefault(require("quick-lru"));
-
-var IndexFile = /*#__PURE__*/function () {
-  /**
-   * @param {filehandle} filehandle
-   * @param {function} [renameRefSeqs]
-   */
-  function IndexFile(_ref) {
-    var filehandle = _ref.filehandle,
-        _ref$renameRefSeqs = _ref.renameRefSeqs,
-        renameRefSeqs = _ref$renameRefSeqs === void 0 ? function (n) {
-      return n;
-    } : _ref$renameRefSeqs;
-    (0, _classCallCheck2.default)(this, IndexFile);
-    (0, _defineProperty2.default)(this, "filehandle", void 0);
-    (0, _defineProperty2.default)(this, "renameRefSeq", void 0);
-    (0, _defineProperty2.default)(this, "_parseCache", void 0);
-    this.filehandle = filehandle;
-    this.renameRefSeq = renameRefSeqs;
-  }
-
-  (0, _createClass2.default)(IndexFile, [{
-    key: "getMetadata",
-    value: function () {
-      var _getMetadata = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var opts,
-            _yield$this$parse,
-            indices,
-            rest,
-            _args = arguments;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
-                _context.next = 3;
-                return this.parse(opts);
-
-              case 3:
-                _yield$this$parse = _context.sent;
-                indices = _yield$this$parse.indices;
-                rest = (0, _objectWithoutProperties2.default)(_yield$this$parse, ["indices"]);
-                return _context.abrupt("return", rest);
-
-              case 7:
-              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 getMetadata() {
-        return _getMetadata.apply(this, arguments);
-      }
-
-      return getMetadata;
-    }()
-  }, {
-    key: "_findFirstData",
-    value: function _findFirstData(currentFdl, virtualOffset) {
-      if (currentFdl) {
-        return currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
-      } else {
-        return virtualOffset;
-      }
+            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 };
     }
-  }, {
-    key: "parse",
-    value: function () {
-      var _parse2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var _this = this;
-
-        var opts,
-            _args2 = arguments;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                opts = _args2.length > 0 && _args2[0] !== undefined ? _args2[0] : {};
-                if (!this._parseCache) this._parseCache = new _abortablePromiseCache.default({
-                  cache: new _quickLru.default({
-                    maxSize: 1
-                  }),
-                  fill: function fill() {
-                    return _this._parse(opts);
-                  }
-                });
-                return _context2.abrupt("return", this._parseCache.get('index', null, opts.signal));
-
-              case 3:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function parse() {
-        return _parse2.apply(this, arguments);
-      }
-
-      return parse;
-    }()
-  }, {
-    key: "hasRefSeq",
-    value: function () {
-      var _hasRefSeq = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(seqId) {
-        var opts,
-            _args3 = arguments;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                opts = _args3.length > 1 && _args3[1] !== undefined ? _args3[1] : {};
-                _context3.next = 3;
-                return this.parse(opts);
-
-              case 3:
-                _context3.t1 = seqId;
-                _context3.t0 = _context3.sent.indices[_context3.t1];
-
-                if (_context3.t0) {
-                  _context3.next = 7;
-                  break;
+};
+var __rest = (this && this.__rest) || function (s, e) {
+    var t = {};
+    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
+        t[p] = s[p];
+    if (s != null && typeof Object.getOwnPropertySymbols === "function")
+        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
+            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
+                t[p[i]] = s[p[i]];
+        }
+    return t;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+var quick_lru_1 = __importDefault(require("quick-lru"));
+var IndexFile = /** @class */ (function () {
+    /**
+     * @param {filehandle} filehandle
+     * @param {function} [renameRefSeqs]
+     */
+    function IndexFile(_a) {
+        var filehandle = _a.filehandle, _b = _a.renameRefSeqs, renameRefSeqs = _b === void 0 ? function (n) { return n; } : _b;
+        this.filehandle = filehandle;
+        this.renameRefSeq = renameRefSeqs;
+    }
+    IndexFile.prototype.getMetadata = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, indices, rest;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0: return [4 /*yield*/, this.parse(opts)];
+                    case 1:
+                        _a = _b.sent(), indices = _a.indices, rest = __rest(_a, ["indices"]);
+                        return [2 /*return*/, rest];
                 }
-
-                _context3.t0 = {};
-
-              case 7:
-                return _context3.abrupt("return", !!_context3.t0.binIndex);
-
-              case 8:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function hasRefSeq(_x) {
-        return _hasRefSeq.apply(this, arguments);
-      }
-
-      return hasRefSeq;
-    }()
-  }]);
-  return IndexFile;
-}();
-
+            });
+        });
+    };
+    IndexFile.prototype._findFirstData = function (currentFdl, virtualOffset) {
+        if (currentFdl) {
+            return currentFdl.compareTo(virtualOffset) > 0
+                ? virtualOffset
+                : currentFdl;
+        }
+        else {
+            return virtualOffset;
+        }
+    };
+    IndexFile.prototype.parse = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
+                if (!this._parseCache) {
+                    this._parseCache = new abortable_promise_cache_1.default({
+                        cache: new quick_lru_1.default({ maxSize: 1 }),
+                        fill: function () { return _this._parse(opts); },
+                    });
+                }
+                return [2 /*return*/, this._parseCache.get('index', null, undefined)];
+            });
+        });
+    };
+    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];
+                }
+            });
+        });
+    };
+    return IndexFile;
+}());
 exports.default = IndexFile;
-//# sourceMappingURL=data:application/json;charset=utf-8;base64,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
+//# sourceMappingURL=indexFile.js.map

package/dist/indexFile.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,oFAA2D;AAC3D,wDAAgC;AAWhC;IAKE;;;OAGG;IACH,mBAAY,EAMX;YALC,UAAU,gBAAA,EACV,qBAAgC,EAAhC,aAAa,mBAAG,UAAC,CAAS,IAAK,OAAA,CAAC,EAAD,CAAC,KAAA;QAKhC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IASY,+BAAW,GAAxB,UAAyB,IAAkB;QAAlB,qBAAA,EAAA,SAAkB;;;;;4BAEZ,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAA7C,KAAuB,SAAsB,EAA3C,OAAO,aAAA,EAAK,IAAI,cAAlB,WAAoB,CAAF;wBACxB,sBAAO,IAAI,EAAA;;;;KACZ;IASD,kCAAc,GAAd,UACE,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE;YACd,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;SACf;aAAM;YACL,OAAO,aAAa,CAAA;SACrB;IACH,CAAC;IAEK,yBAAK,GAAX,UAAY,IAAkB;QAAlB,qBAAA,EAAA,SAAkB;;;;gBAC5B,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;oBACrB,IAAI,CAAC,WAAW,GAAG,IAAI,iCAAqB,CAAC;wBAC3C,KAAK,EAAE,IAAI,mBAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;wBACnC,IAAI,EAAE,cAAM,OAAA,KAAI,CAAC,MAAM,CAAC,IAAI,CAAC,EAAjB,CAAiB;qBAC9B,CAAC,CAAA;iBACH;gBACD,sBAAO,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,IAAI,EAAE,SAAS,CAAC,EAAA;;;KACtD;IAEK,6BAAS,GAAf,UAAgB,KAAa,EAAE,IAAkB;QAAlB,qBAAA,EAAA,SAAkB;;;;4BACpC,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;4BAAjC,sBAAO,CAAC,CAAC,CAAC,CAAC,SAAsB,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,EAAA;;;;KAClE;IACH,gBAAC;AAAD,CAAC,AAlED,IAkEC"}

package/dist/tabixIndexedFile.d.ts

@@ -2,6 +2,12 @@
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options } from './indexFile';
 import Chunk from './chunk';
+declare type GetLinesCallback = (line: string, fileOffset: number) => void;
+interface GetLinesOpts {
+    [key: string]: unknown;
+    signal?: AbortSignal;
+    lineCallback: GetLinesCallback;
+}
 export default class TabixIndexedFile {
     private filehandle;
     private index;
@@ -41,10 +47,7 @@ export default class TabixIndexedFile {
      * @param {function|object} lineCallback callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
      * @returns {Promise} resolved when the whole read is finished, rejected on error
      */
-    getLines(refName: string, start: number, end: number, opts: {
-        signal?: AbortSignal;
-        lineCallback: Function;
-    } | Function): Promise<void>;
+    getLines(refName: string, start: number, end: number, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
     getMetadata(opts?: Options): Promise<any>;
     /**
      * get a buffer containing the "header" region of
@@ -112,3 +115,4 @@ export default class TabixIndexedFile {
      */
     readChunk(chunk: Chunk, opts?: Options): Promise<any>;
 }
+export {};