@gmod/tabix 1.5.3 → 1.5.5

package/dist/indexFile.js

@@ -8,33 +8,6 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         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 __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)
@@ -50,33 +23,25 @@ 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 () {
+const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+const quick_lru_1 = __importDefault(require("quick-lru"));
+class IndexFile {
     /**
      * @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;
+    constructor({ filehandle, renameRefSeqs = (n) => n, }) {
         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];
-                }
-            });
+    getMetadata(opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            // eslint-disable-next-line @typescript-eslint/no-unused-vars
+            const _a = yield this.parse(opts), { indices } = _a, rest = __rest(_a, ["indices"]);
+            return rest;
         });
-    };
-    IndexFile.prototype._findFirstData = function (currentFdl, virtualOffset) {
+    }
+    _findFirstData(currentFdl, virtualOffset) {
         if (currentFdl) {
             return currentFdl.compareTo(virtualOffset) > 0
                 ? virtualOffset
@@ -85,34 +50,23 @@ var IndexFile = /** @class */ (function () {
         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)];
-            });
+    }
+    parse(opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            if (!this._parseCache) {
+                this._parseCache = new abortable_promise_cache_1.default({
+                    cache: new quick_lru_1.default({ maxSize: 1 }),
+                    fill: () => this._parse(opts),
+                });
+            }
+            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];
-                }
-            });
+    }
+    hasRefSeq(seqId, opts = {}) {
+        return __awaiter(this, void 0, void 0, function* () {
+            return !!((yield this.parse(opts)).indices[seqId] || {}).binIndex;
         });
-    };
-    return IndexFile;
-}());
+    }
+}
 exports.default = IndexFile;
 //# sourceMappingURL=indexFile.js.map

package/dist/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,sFAA2D;AAC3D,0DAAgC;AAWhC,MAA8B,SAAS;IAKrC;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IASY,WAAW,CAAC,OAAgB,EAAE;;YACzC,6DAA6D;YAC7D,MAAM,KAAuB,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAA7C,EAAE,OAAO,OAAoC,EAA/B,IAAI,cAAlB,WAAoB,CAAyB,CAAA;YACnD,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IASD,cAAc,CACZ,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,KAAK,CAAC,OAAgB,EAAE;;YAC5B,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;gBACrB,IAAI,CAAC,WAAW,GAAG,IAAI,iCAAqB,CAAC;oBAC3C,KAAK,EAAE,IAAI,mBAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;oBACnC,IAAI,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC;iBAC9B,CAAC,CAAA;aACH;YACD,OAAO,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,IAAI,EAAE,SAAS,CAAC,CAAA;QACvD,CAAC;KAAA;IAEK,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;YAC/C,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;QACnE,CAAC;KAAA;CACF;AAlED,4BAkEC"}

package/dist/tabixIndexedFile.d.ts

@@ -2,7 +2,7 @@
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options } from './indexFile';
 import Chunk from './chunk';
-declare type GetLinesCallback = (line: string, fileOffset: number) => void;
+type GetLinesCallback = (line: string, fileOffset: number) => void;
 interface GetLinesOpts {
     [key: string]: unknown;
     signal?: AbortSignal;