@gmod/bbi 2.0.2 → 2.0.4

package/CHANGELOG.md

@@ -1,6 +1,14 @@
-## [2.0.2](https://github.com/GMOD/bbi-js/compare/v2.0.1...v2.0.2) (2022-07-18)
+## [2.0.4](https://github.com/GMOD/bbi-js/compare/v2.0.3...v2.0.4) (2022-10-15)
+
+
 
+- Use plain TextDecoder for decoding autoSql
 
+## [2.0.3](https://github.com/GMOD/bbi-js/compare/v2.0.2...v2.0.3) (2022-10-10)
+
+- Add BigInt64 polyfill for older safari
+
+## [2.0.2](https://github.com/GMOD/bbi-js/compare/v2.0.1...v2.0.2) (2022-07-18)
 
 - Make basesCovered a number instead of BigInt
 

package/dist/bbi.js

@@ -55,6 +55,9 @@ var operators_1 = require("rxjs/operators");
 var blockView_1 = require("./blockView");
 var BIG_WIG_MAGIC = -2003829722;
 var 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
@@ -187,9 +190,7 @@ var BBI = /** @class */ (function () {
                         }
                         if (asOffset) {
                             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 [2 /*return*/, this._getMainHeader(opts, requestSize * 2)];

package/dist/bbi.js.map

@@ -1 +1 @@
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package/dist/bigint-polyfill/polyfill.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/bigint-polyfill/polyfill.js

@@ -0,0 +1,24 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+var pure_1 = require("./pure");
+if (!('getBigInt64' in DataView)) {
+    DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
+        return (0, pure_1.getBigInt64)(this, byteOffset, littleEndian);
+    };
+}
+if (!('getBigUint64' in DataView)) {
+    DataView.prototype.getBigUint64 = function (byteOffset, littleEndian) {
+        return (0, pure_1.getBigUint64)(this, byteOffset, littleEndian);
+    };
+}
+if (!('setBigInt64' in DataView)) {
+    DataView.prototype.setBigInt64 = function (byteOffset, value, littleEndian) {
+        (0, pure_1.setBigInt64)(this, byteOffset, value, littleEndian);
+    };
+}
+if (!('setBigUint64' in DataView)) {
+    DataView.prototype.setBigUint64 = function (byteOffset, value, littleEndian) {
+        (0, pure_1.setBigUint64)(this, byteOffset, value, littleEndian);
+    };
+}
+//# sourceMappingURL=polyfill.js.map

package/dist/bigint-polyfill/polyfill.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":";;AAAA,+BAA6E;AAE7E,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE;IAChC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,IAAA,kBAAW,EAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;CACF;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE;IACjC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,IAAA,mBAAY,EAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;CACF;AAED,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE;IAChC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,KAAK,EAAE,YAAY;QACxE,IAAA,kBAAW,EAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;CACF;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE;IACjC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,KAAK,EAAE,YAAY;QACzE,IAAA,mBAAY,EAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;CACF"}

package/dist/bigint-polyfill/pure.d.ts

@@ -0,0 +1,4 @@
+export declare function getBigInt64(dataView: DataView, byteOffset: number, littleEndian: boolean | undefined): bigint;
+export declare function getBigUint64(dataView: DataView, byteOffset: number, littleEndian: boolean | undefined): bigint;
+export declare function setBigInt64(dataView: DataView, byteOffset: number, value: bigint, littleEndian: boolean | undefined): void;
+export declare function setBigUint64(dataView: DataView, byteOffset: number, value: bigint, littleEndian: boolean | undefined): void;

package/dist/bigint-polyfill/pure.js

@@ -0,0 +1,53 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.setBigUint64 = exports.setBigInt64 = exports.getBigUint64 = exports.getBigInt64 = void 0;
+var BigInt32 = BigInt(32);
+function getBigInt64(dataView, byteOffset, littleEndian) {
+    var littleEndianMask = Number(!!littleEndian);
+    var bigEndianMask = Number(!littleEndian);
+    return ((BigInt(dataView.getInt32(byteOffset, littleEndian) * bigEndianMask +
+        dataView.getInt32(byteOffset + 4, littleEndian) * littleEndianMask) <<
+        BigInt32) |
+        BigInt(dataView.getUint32(byteOffset, littleEndian) * littleEndianMask +
+            dataView.getUint32(byteOffset + 4, littleEndian) * bigEndianMask));
+}
+exports.getBigInt64 = getBigInt64;
+function getBigUint64(dataView, byteOffset, littleEndian) {
+    var a = dataView.getUint32(byteOffset, littleEndian);
+    var b = dataView.getUint32(byteOffset + 4, littleEndian);
+    var littleEndianMask = Number(!!littleEndian);
+    var bigEndianMask = Number(!littleEndian);
+    // This branch-less optimization is 77x faster than normal ternary operator.
+    // and only 3% slower than native implementation
+    // https://jsbench.me/p8kyhg1eqv/1
+    return ((BigInt(a * bigEndianMask + b * littleEndianMask) << BigInt32) |
+        BigInt(a * littleEndianMask + b * bigEndianMask));
+}
+exports.getBigUint64 = getBigUint64;
+function setBigInt64(dataView, byteOffset, value, littleEndian) {
+    var hi = Number(value >> BigInt32);
+    var lo = Number(value & BigInt(0xffffffff));
+    if (littleEndian) {
+        dataView.setInt32(byteOffset + 4, hi, littleEndian);
+        dataView.setUint32(byteOffset, lo, littleEndian);
+    }
+    else {
+        dataView.setInt32(byteOffset, hi, littleEndian);
+        dataView.setUint32(byteOffset + 4, lo, littleEndian);
+    }
+}
+exports.setBigInt64 = setBigInt64;
+function setBigUint64(dataView, byteOffset, value, littleEndian) {
+    var hi = Number(value >> BigInt32);
+    var lo = Number(value & BigInt(0xffffffff));
+    if (littleEndian) {
+        dataView.setUint32(byteOffset + 4, hi, littleEndian);
+        dataView.setUint32(byteOffset, lo, littleEndian);
+    }
+    else {
+        dataView.setUint32(byteOffset, hi, littleEndian);
+        dataView.setUint32(byteOffset + 4, lo, littleEndian);
+    }
+}
+exports.setBigUint64 = setBigUint64;
+//# sourceMappingURL=pure.js.map

package/dist/bigint-polyfill/pure.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pure.js","sourceRoot":"","sources":["../../src/bigint-polyfill/pure.ts"],"names":[],"mappings":";;;AAAA,IAAM,QAAQ,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;AAE3B,SAAgB,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,IAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,IAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,OAAO,CACL,CAAC,MAAM,CACL,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,aAAa;QACzD,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,gBAAgB,CACrE;QACC,QAAQ,CAAC;QACX,MAAM,CACJ,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,gBAAgB;YAC7D,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,aAAa,CACnE,CACF,CAAA;AACH,CAAC;AAnBD,kCAmBC;AAED,SAAgB,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,IAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,CAAA;IACtD,IAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,CAAA;IAE1D,IAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,IAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,4EAA4E;IAC5E,gDAAgD;IAChD,kCAAkC;IAClC,OAAO,CACL,CAAC,MAAM,CAAC,CAAC,GAAG,aAAa,GAAG,CAAC,GAAG,gBAAgB,CAAC,IAAI,QAAQ,CAAC;QAC9D,MAAM,CAAC,CAAC,GAAG,gBAAgB,GAAG,CAAC,GAAG,aAAa,CAAC,CACjD,CAAA;AACH,CAAC;AAlBD,oCAkBC;AAED,SAAgB,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,IAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,IAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE;QAChB,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACnD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACjD;SAAM;QACL,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAC/C,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACrD;AACH,CAAC;AAhBD,kCAgBC;AAED,SAAgB,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,IAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,IAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE;QAChB,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACpD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACjD;SAAM;QACL,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAChD,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACrD;AACH,CAAC;AAhBD,oCAgBC"}

package/dist/blockView.js

@@ -202,7 +202,7 @@ var BlockView = /** @class */ (function () {
     }
     BlockView.prototype.readWigData = function (chrName, start, end, observer, opts) {
         return __awaiter(this, void 0, void 0, function () {
-            var _a, refsByName, bbi, cirTreeOffset, isBigEndian, chrId_1, request_1, off, buffer, cirBlockSize_1, blocksToFetch_1, outstanding_1, cirFobRecur2_1, filterFeats_1, cirFobStartFetch_1, cirFobRecur_1, e_1;
+            var _a, refsByName, bbi, cirTreeOffset, isBigEndian, chrId_1, request_1, buffer, cirBlockSize_1, blocksToFetch_1, outstanding_1, cirFobRecur2_1, filterFeats_1, cirFobStartFetch_1, cirFobRecur_1, e_1;
             var _this = this;
             return __generator(this, function (_b) {
                 switch (_b.label) {
@@ -215,8 +215,7 @@ var BlockView = /** @class */ (function () {
                         }
                         request_1 = { chrId: chrId_1, start: start, end: end };
                         if (!this.cirTreePromise) {
-                            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);
                         }
                         return [4 /*yield*/, this.cirTreePromise];
                     case 1:

package/dist/blockView.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -1,3 +1,4 @@
+import './bigint-polyfill/polyfill';
 export { BigWig } from './bigwig';
 export { BigBed } from './bigbed';
 export { Feature, Header, RequestOptions } from './bbi';

package/dist/index.js

@@ -1,6 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigBed = exports.BigWig = void 0;
+// from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
+// license:MIT
+// needed for browsers including safari 14
+require("./bigint-polyfill/polyfill");
 var bigwig_1 = require("./bigwig");
 Object.defineProperty(exports, "BigWig", { enumerable: true, get: function () { return bigwig_1.BigWig; } });
 var bigbed_1 = require("./bigbed");

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,mCAAiC;AAAxB,gGAAA,MAAM,OAAA;AACf,mCAAiC;AAAxB,gGAAA,MAAM,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,2FAA2F;AAC3F,cAAc;AACd,0CAA0C;AAC1C,sCAAmC;AACnC,mCAAiC;AAAxB,gGAAA,MAAM,OAAA;AACf,mCAAiC;AAAxB,gGAAA,MAAM,OAAA"}

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/bigint-polyfill/polyfill.d.ts

@@ -0,0 +1 @@
+export {};

package/esm/bigint-polyfill/polyfill.js

@@ -0,0 +1,22 @@
+import { getBigInt64, getBigUint64, setBigInt64, setBigUint64 } from './pure';
+if (!('getBigInt64' in DataView)) {
+    DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
+        return getBigInt64(this, byteOffset, littleEndian);
+    };
+}
+if (!('getBigUint64' in DataView)) {
+    DataView.prototype.getBigUint64 = function (byteOffset, littleEndian) {
+        return getBigUint64(this, byteOffset, littleEndian);
+    };
+}
+if (!('setBigInt64' in DataView)) {
+    DataView.prototype.setBigInt64 = function (byteOffset, value, littleEndian) {
+        setBigInt64(this, byteOffset, value, littleEndian);
+    };
+}
+if (!('setBigUint64' in DataView)) {
+    DataView.prototype.setBigUint64 = function (byteOffset, value, littleEndian) {
+        setBigUint64(this, byteOffset, value, littleEndian);
+    };
+}
+//# sourceMappingURL=polyfill.js.map

package/esm/bigint-polyfill/polyfill.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"polyfill.js","sourceRoot":"","sources":["../../src/bigint-polyfill/polyfill.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAE7E,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE;IAChC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,YAAY;QACjE,OAAO,WAAW,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;CACF;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE;IACjC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,YAAY;QAClE,OAAO,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;CACF;AAED,IAAI,CAAC,CAAC,aAAa,IAAI,QAAQ,CAAC,EAAE;IAChC,QAAQ,CAAC,SAAS,CAAC,WAAW,GAAG,UAAU,UAAU,EAAE,KAAK,EAAE,YAAY;QACxE,WAAW,CAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,YAAY,CAAC,CAAA;IACpD,CAAC,CAAA;CACF;AAED,IAAI,CAAC,CAAC,cAAc,IAAI,QAAQ,CAAC,EAAE;IACjC,QAAQ,CAAC,SAAS,CAAC,YAAY,GAAG,UAAU,UAAU,EAAE,KAAK,EAAE,YAAY;QACzE,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,KAAK,EAAE,YAAY,CAAC,CAAA;IACrD,CAAC,CAAA;CACF"}

package/esm/bigint-polyfill/pure.d.ts

@@ -0,0 +1,4 @@
+export declare function getBigInt64(dataView: DataView, byteOffset: number, littleEndian: boolean | undefined): bigint;
+export declare function getBigUint64(dataView: DataView, byteOffset: number, littleEndian: boolean | undefined): bigint;
+export declare function setBigInt64(dataView: DataView, byteOffset: number, value: bigint, littleEndian: boolean | undefined): void;
+export declare function setBigUint64(dataView: DataView, byteOffset: number, value: bigint, littleEndian: boolean | undefined): void;

package/esm/bigint-polyfill/pure.js

@@ -0,0 +1,46 @@
+const BigInt32 = BigInt(32);
+export function getBigInt64(dataView, byteOffset, littleEndian) {
+    const littleEndianMask = Number(!!littleEndian);
+    const bigEndianMask = Number(!littleEndian);
+    return ((BigInt(dataView.getInt32(byteOffset, littleEndian) * bigEndianMask +
+        dataView.getInt32(byteOffset + 4, littleEndian) * littleEndianMask) <<
+        BigInt32) |
+        BigInt(dataView.getUint32(byteOffset, littleEndian) * littleEndianMask +
+            dataView.getUint32(byteOffset + 4, littleEndian) * bigEndianMask));
+}
+export function getBigUint64(dataView, byteOffset, littleEndian) {
+    const a = dataView.getUint32(byteOffset, littleEndian);
+    const b = dataView.getUint32(byteOffset + 4, littleEndian);
+    const littleEndianMask = Number(!!littleEndian);
+    const bigEndianMask = Number(!littleEndian);
+    // This branch-less optimization is 77x faster than normal ternary operator.
+    // and only 3% slower than native implementation
+    // https://jsbench.me/p8kyhg1eqv/1
+    return ((BigInt(a * bigEndianMask + b * littleEndianMask) << BigInt32) |
+        BigInt(a * littleEndianMask + b * bigEndianMask));
+}
+export function setBigInt64(dataView, byteOffset, value, littleEndian) {
+    const hi = Number(value >> BigInt32);
+    const lo = Number(value & BigInt(0xffffffff));
+    if (littleEndian) {
+        dataView.setInt32(byteOffset + 4, hi, littleEndian);
+        dataView.setUint32(byteOffset, lo, littleEndian);
+    }
+    else {
+        dataView.setInt32(byteOffset, hi, littleEndian);
+        dataView.setUint32(byteOffset + 4, lo, littleEndian);
+    }
+}
+export function setBigUint64(dataView, byteOffset, value, littleEndian) {
+    const hi = Number(value >> BigInt32);
+    const lo = Number(value & BigInt(0xffffffff));
+    if (littleEndian) {
+        dataView.setUint32(byteOffset + 4, hi, littleEndian);
+        dataView.setUint32(byteOffset, lo, littleEndian);
+    }
+    else {
+        dataView.setUint32(byteOffset, hi, littleEndian);
+        dataView.setUint32(byteOffset + 4, lo, littleEndian);
+    }
+}
+//# sourceMappingURL=pure.js.map

package/esm/bigint-polyfill/pure.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pure.js","sourceRoot":"","sources":["../../src/bigint-polyfill/pure.ts"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;AAE3B,MAAM,UAAU,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,OAAO,CACL,CAAC,MAAM,CACL,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,aAAa;QACzD,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,gBAAgB,CACrE;QACC,QAAQ,CAAC;QACX,MAAM,CACJ,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,gBAAgB;YAC7D,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,aAAa,CACnE,CACF,CAAA;AACH,CAAC;AAED,MAAM,UAAU,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,CAAA;IACtD,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,CAAA;IAE1D,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,4EAA4E;IAC5E,gDAAgD;IAChD,kCAAkC;IAClC,OAAO,CACL,CAAC,MAAM,CAAC,CAAC,GAAG,aAAa,GAAG,CAAC,GAAG,gBAAgB,CAAC,IAAI,QAAQ,CAAC;QAC9D,MAAM,CAAC,CAAC,GAAG,gBAAgB,GAAG,CAAC,GAAG,aAAa,CAAC,CACjD,CAAA;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE;QAChB,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACnD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACjD;SAAM;QACL,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAC/C,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACrD;AACH,CAAC;AAED,MAAM,UAAU,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE;QAChB,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACpD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACjD;SAAM;QACL,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAChD,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;KACrD;AACH,CAAC"}

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/esm/index.d.ts

@@ -1,3 +1,4 @@
+import './bigint-polyfill/polyfill';
 export { BigWig } from './bigwig';
 export { BigBed } from './bigbed';
 export { Feature, Header, RequestOptions } from './bbi';

package/esm/index.js

@@ -1,3 +1,7 @@
+// from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
+// license:MIT
+// needed for browsers including safari 14
+import './bigint-polyfill/polyfill';
 export { BigWig } from './bigwig';
 export { BigBed } from './bigbed';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAA;AACjC,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,2FAA2F;AAC3F,cAAc;AACd,0CAA0C;AAC1C,OAAO,4BAA4B,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAA;AACjC,OAAO,EAAE,MAAM,EAAE,MAAM,UAAU,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "2.0.2",
+  "version": "2.0.4",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -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)

package/src/bigint-polyfill/polyfill.ts

@@ -0,0 +1,25 @@
+import { getBigInt64, getBigUint64, setBigInt64, setBigUint64 } from './pure'
+
+if (!('getBigInt64' in DataView)) {
+  DataView.prototype.getBigInt64 = function (byteOffset, littleEndian) {
+    return getBigInt64(this, byteOffset, littleEndian)
+  }
+}
+
+if (!('getBigUint64' in DataView)) {
+  DataView.prototype.getBigUint64 = function (byteOffset, littleEndian) {
+    return getBigUint64(this, byteOffset, littleEndian)
+  }
+}
+
+if (!('setBigInt64' in DataView)) {
+  DataView.prototype.setBigInt64 = function (byteOffset, value, littleEndian) {
+    setBigInt64(this, byteOffset, value, littleEndian)
+  }
+}
+
+if (!('setBigUint64' in DataView)) {
+  DataView.prototype.setBigUint64 = function (byteOffset, value, littleEndian) {
+    setBigUint64(this, byteOffset, value, littleEndian)
+  }
+}

package/src/bigint-polyfill/pure.ts

@@ -0,0 +1,78 @@
+const BigInt32 = BigInt(32)
+
+export function getBigInt64(
+  dataView: DataView,
+  byteOffset: number,
+  littleEndian: boolean | undefined,
+): bigint {
+  const littleEndianMask = Number(!!littleEndian)
+  const bigEndianMask = Number(!littleEndian)
+
+  return (
+    (BigInt(
+      dataView.getInt32(byteOffset, littleEndian) * bigEndianMask +
+        dataView.getInt32(byteOffset + 4, littleEndian) * littleEndianMask,
+    ) <<
+      BigInt32) |
+    BigInt(
+      dataView.getUint32(byteOffset, littleEndian) * littleEndianMask +
+        dataView.getUint32(byteOffset + 4, littleEndian) * bigEndianMask,
+    )
+  )
+}
+
+export function getBigUint64(
+  dataView: DataView,
+  byteOffset: number,
+  littleEndian: boolean | undefined,
+): bigint {
+  const a = dataView.getUint32(byteOffset, littleEndian)
+  const b = dataView.getUint32(byteOffset + 4, littleEndian)
+
+  const littleEndianMask = Number(!!littleEndian)
+  const bigEndianMask = Number(!littleEndian)
+
+  // This branch-less optimization is 77x faster than normal ternary operator.
+  // and only 3% slower than native implementation
+  // https://jsbench.me/p8kyhg1eqv/1
+  return (
+    (BigInt(a * bigEndianMask + b * littleEndianMask) << BigInt32) |
+    BigInt(a * littleEndianMask + b * bigEndianMask)
+  )
+}
+
+export function setBigInt64(
+  dataView: DataView,
+  byteOffset: number,
+  value: bigint,
+  littleEndian: boolean | undefined,
+) {
+  const hi = Number(value >> BigInt32)
+  const lo = Number(value & BigInt(0xffffffff))
+
+  if (littleEndian) {
+    dataView.setInt32(byteOffset + 4, hi, littleEndian)
+    dataView.setUint32(byteOffset, lo, littleEndian)
+  } else {
+    dataView.setInt32(byteOffset, hi, littleEndian)
+    dataView.setUint32(byteOffset + 4, lo, littleEndian)
+  }
+}
+
+export function setBigUint64(
+  dataView: DataView,
+  byteOffset: number,
+  value: bigint,
+  littleEndian: boolean | undefined,
+) {
+  const hi = Number(value >> BigInt32)
+  const lo = Number(value & BigInt(0xffffffff))
+
+  if (littleEndian) {
+    dataView.setUint32(byteOffset + 4, hi, littleEndian)
+    dataView.setUint32(byteOffset, lo, littleEndian)
+  } else {
+    dataView.setUint32(byteOffset, hi, littleEndian)
+    dataView.setUint32(byteOffset + 4, lo, littleEndian)
+  }
+}

package/src/blockView.ts

@@ -16,6 +16,8 @@ interface CoordRequest {
   end: number
 }
 interface DataBlock {
+  blockOffset: bigint
+  blockSize: bigint
   startChrom: number
   endChrom: number
   startBase: number
@@ -200,8 +202,13 @@ 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
@@ -218,7 +225,10 @@ export class BlockView {
         try {
           const data = cirBlockData.subarray(offset)
 
-          const p = this.leafParser.parse(data)
+          const p = this.leafParser.parse(data) as {
+            blocksToFetch: DataBlock[]
+            recurOffsets: DataBlock[]
+          }
           if (p.blocksToFetch) {
             blocksToFetch = blocksToFetch.concat(
               p.blocksToFetch
@@ -232,7 +242,7 @@ export class BlockView {
           if (p.recurOffsets) {
             const recurOffsets = p.recurOffsets
               .filter(filterFeats)
-              .map((l: { blockOffset: bigint }) => Number(l.blockOffset))
+              .map(l => Number(l.blockOffset))
             if (recurOffsets.length > 0) {
               cirFobRecur(recurOffsets, level + 1)
             }

package/src/index.ts

@@ -1,3 +1,7 @@
+// from https://github.com/yume-chan/ya-webadb/blob/main/libraries/dataview-bigint-polyfill
+// license:MIT
+// needed for browsers including safari 14
+import './bigint-polyfill/polyfill'
 export { BigWig } from './bigwig'
 export { BigBed } from './bigbed'
 export { Feature, Header, RequestOptions } from './bbi'