@gmod/bbi 2.0.3 → 2.0.5

package/dist/blockView.js.map

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

@@ -5,8 +5,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
  * Adapted from a combination of Range and _Compound in the
  * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
  */
-var Range = /** @class */ (function () {
-    function Range(arg1, arg2) {
+class Range {
+    constructor(arg1, arg2) {
         this.ranges =
             arguments.length === 2
                 ? [{ min: arg1, max: arg2 }]
@@ -14,36 +14,36 @@ var Range = /** @class */ (function () {
                     ? Object.assign({}, arg1)
                     : [arg1];
     }
-    Range.prototype.min = function () {
+    min() {
         return this.ranges[0].min;
-    };
-    Range.prototype.max = function () {
+    }
+    max() {
         return this.ranges[this.ranges.length - 1].max;
-    };
-    Range.prototype.contains = function (pos) {
-        for (var s = 0; s < this.ranges.length; s += 1) {
-            var r = this.ranges[s];
+    }
+    contains(pos) {
+        for (let s = 0; s < this.ranges.length; s += 1) {
+            const r = this.ranges[s];
             if (r.min <= pos && r.max >= pos) {
                 return true;
             }
         }
         return false;
-    };
-    Range.prototype.isContiguous = function () {
+    }
+    isContiguous() {
         return this.ranges.length > 1;
-    };
-    Range.prototype.getRanges = function () {
-        return this.ranges.map(function (r) { return new Range(r.min, r.max); });
-    };
-    Range.prototype.toString = function () {
-        return this.ranges.map(function (r) { return "[".concat(r.min, "-").concat(r.max, "]"); }).join(',');
-    };
-    Range.prototype.union = function (s1) {
-        var ranges = this.getRanges().concat(s1.getRanges()).sort(this.rangeOrder);
-        var oranges = [];
-        var current = ranges[0];
-        for (var i = 1; i < ranges.length; i += 1) {
-            var nxt = ranges[i];
+    }
+    getRanges() {
+        return this.ranges.map((r) => new Range(r.min, r.max));
+    }
+    toString() {
+        return this.ranges.map((r) => `[${r.min}-${r.max}]`).join(',');
+    }
+    union(s1) {
+        const ranges = this.getRanges().concat(s1.getRanges()).sort(this.rangeOrder);
+        const oranges = [];
+        let current = ranges[0];
+        for (let i = 1; i < ranges.length; i += 1) {
+            const nxt = ranges[i];
             if (nxt.min() > current.max() + 1) {
                 oranges.push(current);
                 current = nxt;
@@ -57,23 +57,23 @@ var Range = /** @class */ (function () {
             return oranges[0];
         }
         return new Range(oranges);
-    };
-    Range.prototype.intersection = function (arg) {
+    }
+    intersection(arg) {
         // eslint-disable-next-line @typescript-eslint/no-this-alias
-        var s0 = this;
-        var s1 = arg;
-        var r0 = this.ranges();
-        var r1 = s1.ranges();
-        var l0 = r0.length;
-        var l1 = r1.length;
-        var i0 = 0;
-        var i1 = 0;
-        var or = [];
+        let s0 = this;
+        let s1 = arg;
+        const r0 = this.ranges();
+        const r1 = s1.ranges();
+        const l0 = r0.length;
+        const l1 = r1.length;
+        let i0 = 0;
+        let i1 = 0;
+        const or = [];
         while (i0 < l0 && i1 < l1) {
             s0 = r0[i0];
             s1 = r1[i1];
-            var lapMin = Math.max(s0.min(), s1.min());
-            var lapMax = Math.min(s0.max(), s1.max());
+            const lapMin = Math.max(s0.min(), s1.min());
+            const lapMax = Math.min(s0.max(), s1.max());
             if (lapMax >= lapMin) {
                 or.push(new Range(lapMin, lapMax));
             }
@@ -91,19 +91,19 @@ var Range = /** @class */ (function () {
             return or[0];
         }
         return new Range(or);
-    };
-    Range.prototype.coverage = function () {
-        var tot = 0;
-        var rl = this.ranges();
-        for (var ri = 0; ri < rl.length; ri += 1) {
-            var r = rl[ri];
+    }
+    coverage() {
+        let tot = 0;
+        const rl = this.ranges();
+        for (let ri = 0; ri < rl.length; ri += 1) {
+            const r = rl[ri];
             tot += r.max() - r.min() + 1;
         }
         return tot;
-    };
-    Range.prototype.rangeOrder = function (tmpa, tmpb) {
-        var a = tmpa;
-        var b = tmpb;
+    }
+    rangeOrder(tmpa, tmpb) {
+        let a = tmpa;
+        let b = tmpb;
         if (arguments.length < 2) {
             b = a;
             // eslint-disable-next-line @typescript-eslint/no-this-alias
@@ -122,8 +122,7 @@ var Range = /** @class */ (function () {
             return 1;
         }
         return 0;
-    };
-    return Range;
-}());
+    }
+}
 exports.default = Range;
 //# sourceMappingURL=range.js.map

package/dist/range.js.map

@@ -1 +1 @@
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package/dist/unzip-pako.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.unzip = void 0;
-var pako_1 = require("pako");
+const pako_1 = require("pako");
 function unzip(input) {
     return (0, pako_1.inflateRaw)(input.subarray(2));
 }

package/dist/unzip-pako.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AAAA,6BAAiC;AAEjC,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,IAAA,iBAAU,EAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC;AAFD,sBAEC"}
+{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AAAA,+BAAiC;AAEjC,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,IAAA,iBAAU,EAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC;AAFD,sBAEC"}

package/dist/unzip.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.unzip = void 0;
-var zlib_1 = require("zlib");
+const zlib_1 = require("zlib");
 Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.inflateSync; } });
 //# sourceMappingURL=unzip.js.map

package/dist/unzip.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAAkC;AACV,sFADf,kBAAW,OACS"}
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,+BAAkC;AACV,sFADf,kBAAW,OACS"}

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) {
@@ -23,54 +8,24 @@ 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.abortBreakPoint = exports.checkAbortSignal = exports.groupBlocks = exports.AbortError = void 0;
 /* eslint no-bitwise: ["error", { "allow": ["|"] }] */
-var AbortError = /** @class */ (function (_super) {
-    __extends(AbortError, _super);
-    function AbortError(message) {
-        var _this = _super.call(this, message) || this;
-        _this.code = 'ERR_ABORTED';
-        return _this;
+class AbortError extends Error {
+    constructor(message) {
+        super(message);
+        this.code = 'ERR_ABORTED';
     }
-    return AbortError;
-}(Error));
+}
 exports.AbortError = AbortError;
 // sort blocks by file offset and
 // group blocks that are within 2KB of eachother
 function groupBlocks(blocks) {
-    blocks.sort(function (b0, b1) { return Number(b0.offset) - Number(b1.offset); });
-    var blockGroups = [];
-    var lastBlock;
-    var lastBlockEnd;
-    for (var i = 0; i < blocks.length; i += 1) {
+    blocks.sort((b0, b1) => Number(b0.offset) - Number(b1.offset));
+    const blockGroups = [];
+    let lastBlock;
+    let lastBlockEnd;
+    for (let i = 0; i < blocks.length; i += 1) {
         if (lastBlock &&
             lastBlockEnd &&
             Number(blocks[i].offset) - lastBlockEnd <= 2000) {
@@ -113,7 +68,7 @@ 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;
         }
@@ -127,16 +82,9 @@ 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;

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,sDAAsD;AACtD,MAAa,UAAW,SAAQ,KAAK;IAGnC,YAAmB,OAAe;QAChC,KAAK,CAAC,OAAO,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,GAAG,aAAa,CAAA;IAC3B,CAAC;CACF;AAPD,gCAOC;AACD,iCAAiC;AACjC,gDAAgD;AAChD,SAAgB,WAAW,CAAC,MAA4C;IACtE,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;IAE9D,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,IAAI,SAAS,CAAA;IACb,IAAI,YAAY,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACzC,IACE,SAAS;YACT,YAAY;YACZ,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,YAAY,IAAI,IAAI,EAC/C;YACA,SAAS,CAAC,MAAM,GAAG,MAAM,CACvB,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;gBACtB,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;gBACxB,YAAY;gBACZ,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAC3B,CAAA;YACD,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;SACjC;aAAM;YACL,WAAW,CAAC,IAAI,CACd,CAAC,SAAS,GAAG;gBACX,MAAM,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;gBACnB,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM;gBACxB,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM;aACzB,CAAC,CACH,CAAA;SACF;QACD,YAAY,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAA;KACnE;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAhCD,kCAgCC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE;QACX,OAAM;KACP;IAED,IAAI,MAAM,CAAC,OAAO,EAAE;QAClB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE;YACvC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;SAChD;aAAM;YACL,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;SACR;KACF;AACH,CAAC;AAfD,4CAeC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAHD,0CAGC"}

package/esm/bbi.js

@@ -5,6 +5,9 @@ import { reduce } from 'rxjs/operators';
 import { BlockView } from './blockView';
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
+function toString(arr) {
+    return new TextDecoder().decode(arr);
+}
 /* get the compiled parsers for different sections of the bigwig file
  *
  * @param isBE - is big endian, typically false
@@ -116,9 +119,7 @@ export class BBI {
         }
         if (asOffset) {
             const off = Number(header.asOffset);
-            header.autoSql = buffer
-                .subarray(off, buffer.indexOf(0, off))
-                .toString('utf8');
+            header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
         }
         if (header.totalSummaryOffset > requestSize) {
             return this._getMainHeader(opts, requestSize * 2);

package/esm/bbi.js.map

@@ -1 +1 @@
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package/esm/blockView.js

@@ -146,8 +146,7 @@ export class BlockView {
             }
             const request = { chrId, start, end };
             if (!this.cirTreePromise) {
-                const off = Number(cirTreeOffset);
-                this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, off, opts);
+                this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, Number(cirTreeOffset), opts);
             }
             const { buffer } = await this.cirTreePromise;
             const cirBlockSize = isBigEndian
@@ -170,7 +169,7 @@ export class BlockView {
                     if (p.recurOffsets) {
                         const recurOffsets = p.recurOffsets
                             .filter(filterFeats)
-                            .map((l) => Number(l.blockOffset));
+                            .map(l => Number(l.blockOffset));
                         if (recurOffsets.length > 0) {
                             cirFobRecur(recurOffsets, level + 1);
                         }

package/esm/blockView.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "2.0.3",
+  "version": "2.0.5",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -26,7 +26,7 @@
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean",
     "build:esm": "tsc --target es2018 --outDir esm --module es2020",
-    "build:es5": "tsc --target es5 --outDir dist --module commonjs",
+    "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",
     "version": "standard-changelog && git add CHANGELOG.md",
@@ -49,25 +49,25 @@
     "rxjs": "^6.5.2"
   },
   "devDependencies": {
-    "@gmod/bed": "^2.0.0",
-    "@types/jest": "^28.1.4",
-    "@types/long": "^4.0.0",
-    "@types/node": "^18.0.0",
+    "@gmod/bed": "^2.1.2",
+    "@types/jest": "^29.1.2",
+    "@types/long": "^5.0.0",
+    "@types/node": "^18.11.0",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.10.0",
-    "@typescript-eslint/parser": "^5.10.0",
+    "@typescript-eslint/eslint-plugin": "^5.40.0",
+    "@typescript-eslint/parser": "^5.40.0",
     "cross-fetch": "^3.0.2",
-    "eslint": "^8.7.0",
+    "eslint": "^8.25.0",
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
     "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^28.1.2",
-    "jest-environment-jsdom": "^28.1.2",
+    "jest": "^29.2.0",
+    "jest-environment-jsdom": "^29.2.0",
     "prettier": "^2.5.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.11",
-    "ts-jest": "^28.0.5",
-    "typescript": "^4.5.2"
+    "ts-jest": "^29.0.3",
+    "typescript": "^4.8.4"
   },
   "publishConfig": {
     "access": "public"

package/src/bbi.ts

@@ -7,6 +7,10 @@ import { BlockView } from './blockView'
 const BIG_WIG_MAGIC = -2003829722
 const BIG_BED_MAGIC = -2021002517
 
+function toString(arr: Uint8Array) {
+  return new TextDecoder().decode(arr)
+}
+
 export interface Feature {
   start: number
   end: number
@@ -190,9 +194,7 @@ export abstract class BBI {
     }
     if (asOffset) {
       const off = Number(header.asOffset)
-      header.autoSql = buffer
-        .subarray(off, buffer.indexOf(0, off))
-        .toString('utf8')
+      header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)))
     }
     if (header.totalSummaryOffset > requestSize) {
       return this._getMainHeader(opts, requestSize * 2)