@gmod/tabix 1.5.3 → 1.5.5

package/dist/util.js

@@ -1,19 +1,4 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 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) {
@@ -23,33 +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 };
-    }
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.optimizeChunks = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = void 0;
 function longToNumber(long) {
@@ -60,13 +18,8 @@ function longToNumber(long) {
     return long.toNumber();
 }
 exports.longToNumber = longToNumber;
-var AbortError = /** @class */ (function (_super) {
-    __extends(AbortError, _super);
-    function AbortError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return AbortError;
-}(Error));
+class AbortError extends Error {
+}
 /**
  * Properly check if the given AbortSignal is aborted.
  * Per the standard, if the signal reads as aborted,
@@ -89,7 +42,7 @@ function checkAbortSignal(signal) {
             throw new DOMException('aborted', 'AbortError');
         }
         else {
-            var e = new AbortError('aborted');
+            const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';
             throw e;
         }
@@ -103,16 +56,9 @@ exports.checkAbortSignal = checkAbortSignal;
  * @param {AbortSignal} signal
  */
 function abortBreakPoint(signal) {
-    return __awaiter(this, void 0, void 0, function () {
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, Promise.resolve()];
-                case 1:
-                    _a.sent();
-                    checkAbortSignal(signal);
-                    return [2 /*return*/];
-            }
-        });
+    return __awaiter(this, void 0, void 0, function* () {
+        yield Promise.resolve();
+        checkAbortSignal(signal);
     });
 }
 exports.abortBreakPoint = abortBreakPoint;
@@ -122,13 +68,13 @@ function canMergeBlocks(chunk1, chunk2) {
 }
 exports.canMergeBlocks = canMergeBlocks;
 function optimizeChunks(chunks, lowest) {
-    var mergedChunks = [];
-    var lastChunk = null;
+    const mergedChunks = [];
+    let lastChunk = null;
     if (chunks.length === 0) {
         return chunks;
     }
     chunks.sort(function (c0, c1) {
-        var dif = c0.minv.blockPosition - c1.minv.blockPosition;
+        const dif = c0.minv.blockPosition - c1.minv.blockPosition;
         if (dif !== 0) {
             return dif;
         }
@@ -136,7 +82,7 @@ function optimizeChunks(chunks, lowest) {
             return c0.minv.dataPosition - c1.minv.dataPosition;
         }
     });
-    chunks.forEach(function (chunk) {
+    chunks.forEach(chunk => {
         if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
             if (lastChunk === null) {
                 mergedChunks.push(chunk);

package/dist/util.js.map

@@ -1 +1 @@
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package/dist/virtualOffset.js

@@ -1,24 +1,20 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fromBytes = void 0;
-var VirtualOffset = /** @class */ (function () {
-    function VirtualOffset(blockPosition, dataPosition) {
+class VirtualOffset {
+    constructor(blockPosition, dataPosition) {
         this.blockPosition = blockPosition; // < offset of the compressed data block
         this.dataPosition = dataPosition; // < offset into the uncompressed data
     }
-    VirtualOffset.prototype.toString = function () {
-        return "".concat(this.blockPosition, ":").concat(this.dataPosition);
-    };
-    VirtualOffset.prototype.compareTo = function (b) {
+    toString() {
+        return `${this.blockPosition}:${this.dataPosition}`;
+    }
+    compareTo(b) {
         return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
-    };
-    VirtualOffset.min = function () {
-        var args = [];
-        for (var _i = 0; _i < arguments.length; _i++) {
-            args[_i] = arguments[_i];
-        }
-        var min;
-        var i = 0;
+    }
+    static min(...args) {
+        let min;
+        let i = 0;
         for (; !min; i += 1) {
             min = args[i];
         }
@@ -28,13 +24,10 @@ var VirtualOffset = /** @class */ (function () {
             }
         }
         return min;
-    };
-    return VirtualOffset;
-}());
+    }
+}
 exports.default = VirtualOffset;
-function fromBytes(bytes, offset, bigendian) {
-    if (offset === void 0) { offset = 0; }
-    if (bigendian === void 0) { bigendian = false; }
+function fromBytes(bytes, offset = 0, bigendian = false) {
     if (bigendian) {
         throw new Error('big-endian virtual file offsets not implemented');
     }

package/dist/virtualOffset.js.map

@@ -1 +1 @@
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package/esm/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;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.3",
+  "version": "1.5.5",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -26,7 +26,7 @@
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean && npm run lint",
     "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es5 --outDir dist",
+    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "preversion": "npm run lint && npm test && npm run build",
     "prepublishOnly": "npm run lint && npm test && npm run build",
@@ -41,28 +41,28 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.3.3",
     "abortable-promise-cache": "^1.4.1",
-    "es6-promisify": "^6.0.1",
-    "generic-filehandle": "^2.0.1",
+    "generic-filehandle": "^3.0.0",
     "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^27.0.3",
+    "@types/jest": "^29.2.4",
     "@types/long": "^4.0.0",
-    "@types/node": "^17.0.25",
+    "@types/node": "^18.0.6",
     "@types/quick-lru": "2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.7.0",
-    "@typescript-eslint/parser": "^5.7.0",
-    "eslint": "^8.13.0",
+    "@typescript-eslint/eslint-plugin": "^5.30.7",
+    "@typescript-eslint/parser": "^5.30.7",
+    "eslint": "^8.20.0",
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
-    "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^27.4.3",
-    "prettier": "^2.5.1",
+    "eslint-plugin-prettier": "^4.2.1",
+    "jest": "^29.3.1",
+    "jest-environment-jsdom": "^29.3.1",
+    "prettier": "^2.7.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.27",
-    "ts-jest": "^27.0.7",
-    "typescript": "^4.5.2"
+    "ts-jest": "^29.0.3",
+    "typescript": "^4.7.4"
   },
   "publishConfig": {
     "access": "public"