@gmod/bbi 1.0.34 → 2.0.1

package/CHANGELOG.md

@@ -1,26 +1,35 @@
-## [1.0.34](https://github.com/GMOD/bbi-js/compare/v1.0.33...v1.0.34) (2022-03-11)
+## [2.0.1](https://github.com/GMOD/bbi-js/compare/v2.0.0...v2.0.1) (2022-07-18)
 
 
-### Reverts
 
-* Revert "Use subarray instead of slice since slice is deprecated under node xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'" ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
+- Bump generic-filehandle 2->3
 
+# [2.0.0](https://github.com/GMOD/bbi-js/compare/v1.0.35...v2.0.0) (2022-07-18)
 
+- Use binary-parser instead of @gmod/binary-parser, with some optimizations.
+  This uses BigInt and TextDecoder, so requires a major version bump
 
-- Back to slice instead of subarray, as subarray returned a UInt8Array instead
-  of a true Buffer
+## [1.0.35](https://github.com/GMOD/bbi-js/compare/v1.0.34...v1.0.35) (2022-04-22)
 
-## [1.0.33](https://github.com/GMOD/bbi-js/compare/v1.0.32...v1.0.33) (2022-02-25)
+- Produce actual ESM module for the "module" field in package.json, was commonJS
+- Add sourceMap:true to tsconfig
 
+## [1.0.34](https://github.com/GMOD/bbi-js/compare/v1.0.33...v1.0.34) (2022-03-11)
+
+### Reverts
 
+- Revert "Use subarray instead of slice since slice is deprecated under node xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'" ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
+
+* Back to slice instead of subarray, as subarray returned a UInt8Array instead
+  of a true Buffer
+
+## [1.0.33](https://github.com/GMOD/bbi-js/compare/v1.0.32...v1.0.33) (2022-02-25)
 
 - Use subarray instead of slice since slice is deprecated under node xref
   'https://nodejs.org/api/buffer.html#bufslicestart-end'"
 
 ## [1.0.32](https://github.com/GMOD/bbi-js/compare/v1.0.31...v1.0.32) (2022-02-16)
 
-
-
 - Use pako to decode on command line instead of using zlib to avoid need to
   manually polyfill zlib
 

package/dist/bbi.d.ts

@@ -49,9 +49,9 @@ export interface RequestOptions {
 }
 export declare abstract class BBI {
     protected bbi: GenericFilehandle;
-    protected headerCache: any;
+    private headerP?;
     protected renameRefSeqs: (a: string) => string;
-    getHeader(opts?: RequestOptions | AbortSignal): any;
+    getHeader(opts?: RequestOptions | AbortSignal): Promise<Header>;
     constructor(options?: {
         filehandle?: GenericFilehandle;
         path?: string;

package/dist/bbi.js

@@ -46,17 +46,12 @@ var __generator = (this && this.__generator) || function (thisArg, body) {
         if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
     }
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BBI = void 0;
-var binary_parser_1 = require("@gmod/binary-parser");
+var binary_parser_1 = require("binary-parser");
 var generic_filehandle_1 = require("generic-filehandle");
 var rxjs_1 = require("rxjs");
 var operators_1 = require("rxjs/operators");
-var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
-var quick_lru_1 = __importDefault(require("quick-lru"));
 var blockView_1 = require("./blockView");
 var BIG_WIG_MAGIC = -2003829722;
 var BIG_BED_MAGIC = -2021002517;
@@ -84,6 +79,7 @@ function getParsers(isBE) {
         .array('zoomLevels', {
         length: 'numZoomLevels',
         type: new binary_parser_1.Parser()
+            .endianess(le)
             .uint32('reductionLevel')
             .uint32('reserved')
             .uint64('dataOffset')
@@ -92,10 +88,10 @@ function getParsers(isBE) {
     var totalSummaryParser = new binary_parser_1.Parser()
         .endianess(le)
         .uint64('basesCovered')
-        .double('scoreMin')
-        .double('scoreMax')
-        .double('scoreSum')
-        .double('scoreSumSquares');
+        .doublele('scoreMin')
+        .doublele('scoreMax')
+        .doublele('scoreSum')
+        .doublele('scoreSumSquares');
     var chromTreeParser = new binary_parser_1.Parser()
         .endianess(le)
         .uint32('magic')
@@ -107,7 +103,8 @@ function getParsers(isBE) {
         .endianess(le)
         .uint8('isLeafNode')
         .skip(1)
-        .uint16('cnt');
+        .uint16('cnt')
+        .saveOffset('offset');
     return {
         chromTreeParser: chromTreeParser,
         totalSummaryParser: totalSummaryParser,
@@ -123,18 +120,9 @@ var BBI = /** @class */ (function () {
      * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
      */
     function BBI(options) {
-        var _this = this;
         if (options === void 0) { options = {}; }
-        this.headerCache = new abortable_promise_cache_1.default({
-            cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: function (params, signal) { return __awaiter(_this, void 0, void 0, function () {
-                return __generator(this, function (_a) {
-                    return [2 /*return*/, this._getHeader(__assign(__assign({}, params), { signal: signal }))];
-                });
-            }); },
-        });
-        var filehandle = options.filehandle, renameRefSeqs = options.renameRefSeqs, path = options.path, url = options.url;
-        this.renameRefSeqs = renameRefSeqs || (function (s) { return s; });
+        var filehandle = options.filehandle, _a = options.renameRefSeqs, renameRefSeqs = _a === void 0 ? function (s) { return s; } : _a, path = options.path, url = options.url;
+        this.renameRefSeqs = renameRefSeqs;
         if (filehandle) {
             this.bbi = filehandle;
         }
@@ -153,9 +141,16 @@ var BBI = /** @class */ (function () {
      * @return a Header object
      */
     BBI.prototype.getHeader = function (opts) {
+        var _this = this;
         if (opts === void 0) { opts = {}; }
         var options = 'aborted' in opts ? { signal: opts } : opts;
-        return this.headerCache.get(JSON.stringify(options), options, options.signal);
+        if (!this.headerP) {
+            this.headerP = this._getHeader(options).catch(function (e) {
+                _this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
     };
     BBI.prototype._getHeader = function (opts) {
         return __awaiter(this, void 0, void 0, function () {
@@ -176,7 +171,7 @@ var BBI = /** @class */ (function () {
     BBI.prototype._getMainHeader = function (opts, requestSize) {
         if (requestSize === void 0) { requestSize = 2000; }
         return __awaiter(this, void 0, void 0, function () {
-            var buffer, isBigEndian, ret, header, tail;
+            var buffer, isBigEndian, ret, header, magic, asOffset, totalSummaryOffset, off, tail;
             return __generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, this.bbi.read(Buffer.alloc(requestSize), 0, requestSize, 0, opts)];
@@ -184,23 +179,24 @@ var BBI = /** @class */ (function () {
                         buffer = (_a.sent()).buffer;
                         isBigEndian = this._isBigEndian(buffer);
                         ret = getParsers(isBigEndian);
-                        header = ret.headerParser.parse(buffer).result;
-                        header.fileType = header.magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig';
-                        if (header.asOffset > requestSize ||
-                            header.totalSummaryOffset > requestSize) {
+                        header = ret.headerParser.parse(buffer);
+                        magic = header.magic, asOffset = header.asOffset, totalSummaryOffset = header.totalSummaryOffset;
+                        header.fileType = magic === BIG_BED_MAGIC ? 'bigbed' : 'bigwig';
+                        if (asOffset > requestSize || totalSummaryOffset > requestSize) {
                             return [2 /*return*/, this._getMainHeader(opts, requestSize * 2)];
                         }
-                        if (header.asOffset) {
+                        if (asOffset) {
+                            off = Number(header.asOffset);
                             header.autoSql = buffer
-                                .slice(header.asOffset, buffer.indexOf(0, header.asOffset))
+                                .subarray(off, buffer.indexOf(0, off))
                                 .toString('utf8');
                         }
                         if (header.totalSummaryOffset > requestSize) {
                             return [2 /*return*/, this._getMainHeader(opts, requestSize * 2)];
                         }
                         if (header.totalSummaryOffset) {
-                            tail = buffer.slice(header.totalSummaryOffset);
-                            header.totalSummary = ret.totalSummaryParser.parse(tail).result;
+                            tail = buffer.subarray(Number(header.totalSummaryOffset));
+                            header.totalSummary = ret.totalSummaryParser.parse(tail);
                         }
                         return [2 /*return*/, __assign(__assign({}, header), { isBigEndian: isBigEndian })];
                 }
@@ -221,7 +217,7 @@ var BBI = /** @class */ (function () {
     // todo: add progress if long running
     BBI.prototype._readChromTree = function (header, opts) {
         return __awaiter(this, void 0, void 0, function () {
-            var isBE, le, refsByNumber, refsByName, chromTreeOffset, unzoomedDataOffset, data, p, keySize, leafNodeParser, nonleafNodeParser, rootNodeOffset, bptReadNode;
+            var isBE, le, refsByNumber, refsByName, unzoomedDataOffset, chromTreeOffset, off, buffer, p, keySize, leafNodeParser, nonleafNodeParser, rootNodeOffset, bptReadNode;
             var _this = this;
             return __generator(this, function (_a) {
                 switch (_a.label) {
@@ -230,43 +226,46 @@ var BBI = /** @class */ (function () {
                         le = isBE ? 'big' : 'little';
                         refsByNumber = [];
                         refsByName = {};
-                        chromTreeOffset = header.chromTreeOffset;
-                        unzoomedDataOffset = header.unzoomedDataOffset;
+                        unzoomedDataOffset = Number(header.unzoomedDataOffset);
+                        chromTreeOffset = Number(header.chromTreeOffset);
                         while (unzoomedDataOffset % 4 !== 0) {
                             unzoomedDataOffset += 1;
                         }
-                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(unzoomedDataOffset - chromTreeOffset), 0, unzoomedDataOffset - chromTreeOffset, chromTreeOffset, opts)];
+                        off = unzoomedDataOffset - chromTreeOffset;
+                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts)];
                     case 1:
-                        data = (_a.sent()).buffer;
+                        buffer = (_a.sent()).buffer;
                         p = getParsers(isBE);
-                        keySize = p.chromTreeParser.parse(data).result.keySize;
+                        keySize = p.chromTreeParser.parse(buffer).keySize;
                         leafNodeParser = new binary_parser_1.Parser()
                             .endianess(le)
                             .string('key', { stripNull: true, length: keySize })
                             .uint32('refId')
-                            .uint32('refSize');
+                            .uint32('refSize')
+                            .saveOffset('offset');
                         nonleafNodeParser = new binary_parser_1.Parser()
                             .endianess(le)
                             .skip(keySize)
-                            .uint64('childOffset');
+                            .uint64('childOffset')
+                            .saveOffset('offset');
                         rootNodeOffset = 32;
                         bptReadNode = function (currentOffset) { return __awaiter(_this, void 0, void 0, function () {
-                            var offset, ret, _a, isLeafNode, cnt, n, leafRet, _b, key, refId, refSize, refRec, nextNodes, n, nonleafRet, childOffset;
-                            return __generator(this, function (_c) {
-                                switch (_c.label) {
+                            var offset, ret, isLeafNode, cnt, n, leafRet, key, refId, refSize, refRec, nextNodes, n, nonleafRet, childOffset;
+                            return __generator(this, function (_a) {
+                                switch (_a.label) {
                                     case 0:
                                         offset = currentOffset;
-                                        if (offset >= data.length) {
+                                        if (offset >= buffer.length) {
                                             throw new Error('reading beyond end of buffer');
                                         }
-                                        ret = p.isLeafNode.parse(data.slice(offset));
-                                        _a = ret.result, isLeafNode = _a.isLeafNode, cnt = _a.cnt;
+                                        ret = p.isLeafNode.parse(buffer.subarray(offset));
+                                        isLeafNode = ret.isLeafNode, cnt = ret.cnt;
                                         offset += ret.offset;
                                         if (!isLeafNode) return [3 /*break*/, 1];
                                         for (n = 0; n < cnt; n += 1) {
-                                            leafRet = leafNodeParser.parse(data.slice(offset));
+                                            leafRet = leafNodeParser.parse(buffer.subarray(offset));
                                             offset += leafRet.offset;
-                                            _b = leafRet.result, key = _b.key, refId = _b.refId, refSize = _b.refSize;
+                                            key = leafRet.key, refId = leafRet.refId, refSize = leafRet.refSize;
                                             refRec = { name: key, id: refId, length: refSize };
                                             refsByName[this.renameRefSeqs(key)] = refId;
                                             refsByNumber[refId] = refRec;
@@ -275,16 +274,15 @@ var BBI = /** @class */ (function () {
                                     case 1:
                                         nextNodes = [];
                                         for (n = 0; n < cnt; n += 1) {
-                                            nonleafRet = nonleafNodeParser.parse(data.slice(offset));
-                                            childOffset = nonleafRet.result.childOffset;
+                                            nonleafRet = nonleafNodeParser.parse(buffer.subarray(offset));
+                                            childOffset = nonleafRet.childOffset;
                                             offset += nonleafRet.offset;
-                                            childOffset -= chromTreeOffset;
-                                            nextNodes.push(bptReadNode(childOffset));
+                                            nextNodes.push(bptReadNode(Number(childOffset) - Number(chromTreeOffset)));
                                         }
                                         return [4 /*yield*/, Promise.all(nextNodes)];
                                     case 2:
-                                        _c.sent();
-                                        _c.label = 3;
+                                        _a.sent();
+                                        _a.label = 3;
                                     case 3: return [2 /*return*/];
                                 }
                             });
@@ -306,15 +304,13 @@ var BBI = /** @class */ (function () {
      */
     BBI.prototype.getUnzoomedView = function (opts) {
         return __awaiter(this, void 0, void 0, function () {
-            var _a, unzoomedIndexOffset, zoomLevels, refsByName, uncompressBufSize, isBigEndian, fileType, nzl, cirLen;
+            var _a, unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType;
             return __generator(this, function (_b) {
                 switch (_b.label) {
                     case 0: return [4 /*yield*/, this.getHeader(opts)];
                     case 1:
-                        _a = _b.sent(), unzoomedIndexOffset = _a.unzoomedIndexOffset, zoomLevels = _a.zoomLevels, refsByName = _a.refsByName, uncompressBufSize = _a.uncompressBufSize, isBigEndian = _a.isBigEndian, fileType = _a.fileType;
-                        nzl = zoomLevels[0];
-                        cirLen = nzl ? nzl.dataOffset - unzoomedIndexOffset : 4000;
-                        return [2 /*return*/, new blockView_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, cirLen, isBigEndian, uncompressBufSize > 0, fileType)];
+                        _a = _b.sent(), unzoomedIndexOffset = _a.unzoomedIndexOffset, refsByName = _a.refsByName, uncompressBufSize = _a.uncompressBufSize, isBigEndian = _a.isBigEndian, fileType = _a.fileType;
+                        return [2 /*return*/, new blockView_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType)];
                 }
             });
         });
@@ -389,3 +385,4 @@ var BBI = /** @class */ (function () {
     return BBI;
 }());
 exports.BBI = BBI;
+//# sourceMappingURL=bbi.js.map

package/dist/bbi.js.map

@@ -0,0 +1 @@
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package/dist/bigbed.d.ts

@@ -3,9 +3,8 @@ import { BlockView } from './blockView';
 export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
 export declare class BigBed extends BBI {
     readIndicesCache: any;
-    constructor(opts?: any);
     readIndices(opts?: AbortSignal | RequestOptions): any;
-    protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
+    protected getView(_scale: number, opts: RequestOptions): Promise<BlockView>;
     private _readIndices;
     private searchExtraIndexBlocks;
     searchExtraIndex(name: string, opts?: RequestOptions): Promise<Feature[]>;

package/dist/bigbed.js

@@ -66,7 +66,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigBed = exports.filterUndef = void 0;
-var binary_parser_1 = require("@gmod/binary-parser");
+var binary_parser_1 = require("binary-parser");
 var rxjs_1 = require("rxjs");
 var operators_1 = require("rxjs/operators");
 var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
@@ -78,8 +78,8 @@ function filterUndef(ts) {
 exports.filterUndef = filterUndef;
 var BigBed = /** @class */ (function (_super) {
     __extends(BigBed, _super);
-    function BigBed(opts) {
-        var _this = _super.call(this, opts) || this;
+    function BigBed() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
         _this.readIndicesCache = new abortable_promise_cache_1.default({
             cache: new quick_lru_1.default({ maxSize: 1 }),
             fill: function (args, signal) { return __awaiter(_this, void 0, void 0, function () {
@@ -101,7 +101,7 @@ var BigBed = /** @class */ (function (_super) {
      * @param abortSignal - an optional AbortSignal to kill operation
      * @return promise for a BlockView
      */
-    BigBed.prototype.getView = function (scale, opts) {
+    BigBed.prototype.getView = function (_scale, opts) {
         return __awaiter(this, void 0, void 0, function () {
             return __generator(this, function (_a) {
                 return [2 /*return*/, this.getUnzoomedView(opts)];
@@ -121,7 +121,7 @@ var BigBed = /** @class */ (function (_super) {
                     case 0: return [4 /*yield*/, this.getHeader(opts)];
                     case 1:
                         _a = _b.sent(), extHeaderOffset = _a.extHeaderOffset, isBigEndian = _a.isBigEndian;
-                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(64), 0, 64, extHeaderOffset)];
+                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(64), 0, 64, Number(extHeaderOffset))];
                     case 2:
                         data = (_b.sent()).buffer;
                         le = isBigEndian ? 'big' : 'little';
@@ -130,7 +130,7 @@ var BigBed = /** @class */ (function (_super) {
                             .uint16('size')
                             .uint16('count')
                             .uint64('offset')
-                            .parse(data).result;
+                            .parse(data);
                         count = ret.count, offset = ret.offset;
                         // no extra index is defined if count==0
                         if (count === 0) {
@@ -138,7 +138,7 @@ var BigBed = /** @class */ (function (_super) {
                         }
                         blocklen = 20;
                         len = blocklen * count;
-                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(len), 0, len, offset)];
+                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(len), 0, len, Number(offset))];
                     case 3:
                         buffer = (_b.sent()).buffer;
                         extParser = new binary_parser_1.Parser()
@@ -150,7 +150,7 @@ var BigBed = /** @class */ (function (_super) {
                             .int16('field');
                         indices = [];
                         for (i = 0; i < count; i += 1) {
-                            indices.push(extParser.parse(buffer.slice(i * blocklen)).result);
+                            indices.push(extParser.parse(buffer.subarray(i * blocklen)));
                         }
                         return [2 /*return*/, indices];
                 }
@@ -182,25 +182,26 @@ var BigBed = /** @class */ (function (_super) {
                             return [2 /*return*/, []];
                         }
                         locs = indices.map(function (index) { return __awaiter(_this, void 0, void 0, function () {
-                            var offset, field, data, p, _a, blockSize, keySize, valSize, bpt, bptReadNode, rootNodeOffset;
+                            var offset, field, data, le, p, _a, blockSize, keySize, valSize, bpt, bptReadNode, rootNodeOffset;
                             var _this = this;
                             return __generator(this, function (_b) {
                                 switch (_b.label) {
                                     case 0:
                                         offset = index.offset, field = index.field;
-                                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(32), 0, 32, offset, opts)];
+                                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(32), 0, 32, Number(offset), opts)];
                                     case 1:
                                         data = (_b.sent()).buffer;
+                                        le = isBigEndian ? 'big' : 'little';
                                         p = new binary_parser_1.Parser()
-                                            .endianess(isBigEndian ? 'big' : 'little')
+                                            .endianess(le)
                                             .int32('magic')
                                             .int32('blockSize')
                                             .int32('keySize')
                                             .int32('valSize')
                                             .uint64('itemCount');
-                                        _a = p.parse(data).result, blockSize = _a.blockSize, keySize = _a.keySize, valSize = _a.valSize;
+                                        _a = p.parse(data), blockSize = _a.blockSize, keySize = _a.keySize, valSize = _a.valSize;
                                         bpt = new binary_parser_1.Parser()
-                                            .endianess(isBigEndian ? 'big' : 'little')
+                                            .endianess(le)
                                             .int8('nodeType')
                                             .skip(1)
                                             .int16('cnt')
@@ -210,12 +211,14 @@ var BigBed = /** @class */ (function (_super) {
                                                 0: new binary_parser_1.Parser().array('leafkeys', {
                                                     length: 'cnt',
                                                     type: new binary_parser_1.Parser()
+                                                        .endianess(le)
                                                         .string('key', { length: keySize, stripNull: true })
                                                         .uint64('offset'),
                                                 }),
                                                 1: new binary_parser_1.Parser().array('keys', {
                                                     length: 'cnt',
                                                     type: new binary_parser_1.Parser()
+                                                        .endianess(le)
                                                         .string('key', { length: keySize, stripNull: true })
                                                         .uint64('offset')
                                                         .uint32('length')
@@ -224,15 +227,16 @@ var BigBed = /** @class */ (function (_super) {
                                             },
                                         });
                                         bptReadNode = function (nodeOffset) { return __awaiter(_this, void 0, void 0, function () {
-                                            var len, buffer, node, lastOffset, i, key, i;
+                                            var val, len, buffer, node, lastOffset, i, key, i;
                                             return __generator(this, function (_a) {
                                                 switch (_a.label) {
                                                     case 0:
+                                                        val = Number(nodeOffset);
                                                         len = 4 + blockSize * (keySize + valSize);
-                                                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(len), 0, len, nodeOffset, opts)];
+                                                        return [4 /*yield*/, this.bbi.read(Buffer.alloc(len), 0, len, val, opts)];
                                                     case 1:
                                                         buffer = (_a.sent()).buffer;
-                                                        node = bpt.parse(buffer).result;
+                                                        node = bpt.parse(buffer);
                                                         if (node.leafkeys) {
                                                             lastOffset = void 0;
                                                             for (i = 0; i < node.leafkeys.length; i += 1) {
@@ -254,7 +258,7 @@ var BigBed = /** @class */ (function (_super) {
                                             });
                                         }); };
                                         rootNodeOffset = 32;
-                                        return [2 /*return*/, bptReadNode(offset + rootNodeOffset)];
+                                        return [2 /*return*/, bptReadNode(Number(offset) + rootNodeOffset)];
                                 }
                             });
                         }); });
@@ -301,9 +305,7 @@ var BigBed = /** @class */ (function (_super) {
                         return [4 /*yield*/, rxjs_1.merge.apply(void 0, res).toPromise()];
                     case 3:
                         ret = _a.sent();
-                        return [2 /*return*/, ret.filter(function (f) {
-                                return f.rest.split('\t')[f.field - 3] === name;
-                            })];
+                        return [2 /*return*/, ret.filter(function (f) { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; })];
                 }
             });
         });
@@ -311,3 +313,4 @@ var BigBed = /** @class */ (function (_super) {
     return BigBed;
 }(bbi_1.BBI));
 exports.BigBed = BigBed;
+//# sourceMappingURL=bigbed.js.map

package/dist/bigbed.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAsC;AACtC,6BAAwC;AACxC,4CAA4C;AAC5C,oFAA2D;AAC3D,wDAAgC;AAEhC,6BAAoD;AAiBpD,SAAgB,WAAW,CAAI,EAAqB;IAClD,OAAO,EAAE,CAAC,MAAM,CAAC,UAAC,CAAgB,IAAa,OAAA,CAAC,CAAC,CAAC,EAAH,CAAG,CAAC,CAAA;AACrD,CAAC;AAFD,kCAEC;AAED;IAA4B,0BAAG;IAA/B;QAAA,qEAwNC;QAvNQ,sBAAgB,GAAG,IAAI,iCAAqB,CAAC;YAClD,KAAK,EAAE,IAAI,mBAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,UAAO,IAAS,EAAE,MAAoB;;oBAC1C,sBAAO,IAAI,CAAC,YAAY,uBAAM,IAAI,KAAE,MAAM,QAAA,IAAG,EAAA;;iBAC9C;SACF,CAAC,CAAA;;IAkNJ,CAAC;IAhNQ,4BAAW,GAAlB,UAAmB,IAAuC;QAAvC,qBAAA,EAAA,SAAuC;QACxD,IAAM,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;QAC3D,OAAO,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAC9B,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,EACvB,OAAO,EACP,OAAO,CAAC,MAAM,CACf,CAAA;IACH,CAAC;IAED;;;;;OAKG;IACa,wBAAO,GAAvB,UACE,MAAc,EACd,IAAoB;;;gBAEpB,sBAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,EAAA;;;KAClC;IAED;;;;OAIG;IACW,6BAAY,GAA1B,UAA2B,IAAoB;;;;;4BACJ,qBAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAA;;wBAA7D,KAAmC,SAA0B,EAA3D,eAAe,qBAAA,EAAE,WAAW,iBAAA;wBACX,qBAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,eAAe,CAAC,CACxB,EAAA;;wBALe,IAAI,GAAK,CAAA,SAKxB,CAAA,OALmB;wBAMd,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;wBACnC,GAAG,GAAG,IAAI,sBAAM,EAAE;6BACrB,SAAS,CAAC,EAAE,CAAC;6BACb,MAAM,CAAC,MAAM,CAAC;6BACd,MAAM,CAAC,OAAO,CAAC;6BACf,MAAM,CAAC,QAAQ,CAAC;6BAChB,KAAK,CAAC,IAAI,CAAC,CAAA;wBAEN,KAAK,GAAa,GAAG,MAAhB,EAAE,MAAM,GAAK,GAAG,OAAR,CAAQ;wBAE7B,wCAAwC;wBACxC,IAAI,KAAK,KAAK,CAAC,EAAE;4BACf,sBAAO,EAAE,EAAA;yBACV;wBAEK,QAAQ,GAAG,EAAE,CAAA;wBACb,GAAG,GAAG,QAAQ,GAAG,KAAK,CAAA;wBACT,qBAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,MAAM,CAAC,MAAM,CAAC,CACf,EAAA;;wBALO,MAAM,GAAK,CAAA,SAKlB,CAAA,OALa;wBAMR,SAAS,GAAG,IAAI,sBAAM,EAAE;6BAC3B,SAAS,CAAC,EAAE,CAAC;6BACb,KAAK,CAAC,MAAM,CAAC;6BACb,KAAK,CAAC,YAAY,CAAC;6BACnB,MAAM,CAAC,QAAQ,CAAC;6BAChB,IAAI,CAAC,CAAC,CAAC;6BACP,KAAK,CAAC,OAAO,CAAC,CAAA;wBACX,OAAO,GAAG,EAAa,CAAA;wBAE7B,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE;4BACjC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;yBAC7D;wBACD,sBAAO,OAAO,EAAA;;;;KACf;IAED;;;;;;;OAOG;IACW,uCAAsB,GAApC,UACE,IAAY,EACZ,IAAyB;QAAzB,qBAAA,EAAA,SAAyB;;;;;;4BAED,qBAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAA;;wBAA1C,WAAW,GAAK,CAAA,SAA0B,CAAA,YAA/B;wBACH,qBAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,EAAA;;wBAAtC,OAAO,GAAG,SAA4B;wBAC5C,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE;4BACnB,sBAAO,EAAE,EAAA;yBACV;wBACK,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,UAAO,KAAU;;;;;;wCAChC,MAAM,GAAY,KAAK,OAAjB,EAAE,KAAK,GAAK,KAAK,MAAV,CAAU;wCACN,qBAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,MAAM,CAAC,EACd,IAAI,CACL,EAAA;;wCANe,IAAI,GAAK,CAAA,SAMxB,CAAA,OANmB;wCAOd,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;wCACnC,CAAC,GAAG,IAAI,sBAAM,EAAE;6CACnB,SAAS,CAAC,EAAE,CAAC;6CACb,KAAK,CAAC,OAAO,CAAC;6CACd,KAAK,CAAC,WAAW,CAAC;6CAClB,KAAK,CAAC,SAAS,CAAC;6CAChB,KAAK,CAAC,SAAS,CAAC;6CAChB,MAAM,CAAC,WAAW,CAAC,CAAA;wCAEhB,KAAkC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,EAA7C,SAAS,eAAA,EAAE,OAAO,aAAA,EAAE,OAAO,aAAA,CAAkB;wCAE/C,GAAG,GAAG,IAAI,sBAAM,EAAE;6CACrB,SAAS,CAAC,EAAE,CAAC;6CACb,IAAI,CAAC,UAAU,CAAC;6CAChB,IAAI,CAAC,CAAC,CAAC;6CACP,KAAK,CAAC,KAAK,CAAC;6CACZ,MAAM,CAAC;4CACN,GAAG,EAAE,UAAU;4CACf,OAAO,EAAE;gDACP,CAAC,EAAE,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE;oDAChC,MAAM,EAAE,KAAK;oDACb,IAAI,EAAE,IAAI,sBAAM,EAAE;yDACf,SAAS,CAAC,EAAE,CAAC;yDACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;yDACnD,MAAM,CAAC,QAAQ,CAAC;iDACpB,CAAC;gDACF,CAAC,EAAE,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,MAAM,EAAE;oDAC5B,MAAM,EAAE,KAAK;oDACb,IAAI,EAAE,IAAI,sBAAM,EAAE;yDACf,SAAS,CAAC,EAAE,CAAC;yDACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;yDACnD,MAAM,CAAC,QAAQ,CAAC;yDAChB,MAAM,CAAC,QAAQ,CAAC;yDAChB,MAAM,CAAC,UAAU,CAAC;iDACtB,CAAC;6CACH;yCACF,CAAC,CAAA;wCAEE,WAAW,GAAG,UAClB,UAAkB;;;;;wDAEZ,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAA;wDACxB,GAAG,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,OAAO,GAAG,OAAO,CAAC,CAAA;wDAC5B,qBAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,GAAG,EACH,IAAI,CACL,EAAA;;wDANO,MAAM,GAAK,CAAA,SAMlB,CAAA,OANa;wDAOR,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;wDAC9B,IAAI,IAAI,CAAC,QAAQ,EAAE;4DACb,UAAU,SAAA,CAAA;4DACd,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;gEACxC,GAAG,GAAK,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,IAArB,CAAqB;gEAChC,IAAI,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,EAAE;oEAC7C,sBAAO,WAAW,CAAC,UAAU,CAAC,EAAA;iEAC/B;gEACD,UAAU,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;6DACrC;4DACD,sBAAO,WAAW,CAAC,UAAU,CAAC,EAAA;yDAC/B;wDACD,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;4DAC5C,IAAI,IAA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package/dist/bigwig.d.ts

@@ -4,9 +4,7 @@ export declare class BigWig extends BBI {
     /**
      * Retrieves a BlockView of a specific zoomLevel
      *
-     * @param refName - The chromosome name
-     * @param start - The start of a region
-     * @param end - The end of a region
+     * @param scale - number
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
      */
     protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;

package/dist/bigwig.js

@@ -62,14 +62,12 @@ var BigWig = /** @class */ (function (_super) {
     /**
      * Retrieves a BlockView of a specific zoomLevel
      *
-     * @param refName - The chromosome name
-     * @param start - The start of a region
-     * @param end - The end of a region
+     * @param scale - number
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
      */
     BigWig.prototype.getView = function (scale, opts) {
         return __awaiter(this, void 0, void 0, function () {
-            var _a, zoomLevels, refsByName, fileSize, isBigEndian, uncompressBufSize, basesPerPx, maxLevel, i, zh, indexLength;
+            var _a, zoomLevels, refsByName, fileSize, isBigEndian, uncompressBufSize, basesPerPx, maxLevel, i, zh, indexOffset;
             return __generator(this, function (_b) {
                 switch (_b.label) {
                     case 0: return [4 /*yield*/, this.getHeader(opts)];
@@ -84,10 +82,8 @@ var BigWig = /** @class */ (function (_super) {
                         for (i = maxLevel; i >= 0; i -= 1) {
                             zh = zoomLevels[i];
                             if (zh && zh.reductionLevel <= 2 * basesPerPx) {
-                                indexLength = i < zoomLevels.length - 1
-                                    ? zoomLevels[i + 1].dataOffset - zh.indexOffset
-                                    : fileSize - 4 - zh.indexOffset;
-                                return [2 /*return*/, new blockView_1.BlockView(this.bbi, refsByName, zh.indexOffset, indexLength, isBigEndian, uncompressBufSize > 0, 'summary')];
+                                indexOffset = Number(zh.indexOffset);
+                                return [2 /*return*/, new blockView_1.BlockView(this.bbi, refsByName, indexOffset, isBigEndian, uncompressBufSize > 0, 'summary')];
                             }
                         }
                         return [2 /*return*/, this.getUnzoomedView(opts)];
@@ -98,3 +94,4 @@ var BigWig = /** @class */ (function (_super) {
     return BigWig;
 }(bbi_1.BBI));
 exports.BigWig = BigWig;
+//# sourceMappingURL=bigwig.js.map

package/dist/bigwig.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,yCAAuC;AACvC,6BAA2C;AAE3C;IAA4B,0BAAG;IAA/B;;IAkCA,CAAC;IAjCC;;;;;OAKG;IACa,wBAAO,GAAvB,UAAwB,KAAa,EAAE,IAAoB;;;;;4BAEvD,qBAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAA;;wBADtB,KACJ,SAA0B,EADpB,UAAU,gBAAA,EAAE,UAAU,gBAAA,EAAE,QAAQ,cAAA,EAAE,WAAW,iBAAA,EAAE,iBAAiB,uBAAA;wBAElE,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;wBACxB,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;wBAChC,IAAI,CAAC,QAAQ,EAAE;4BACb,4EAA4E;4BAC5E,QAAQ,IAAI,CAAC,CAAA;yBACd;wBAED,KAAS,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC/B,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;4BACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;gCACvC,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;gCAE1C,sBAAO,IAAI,qBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,EAAA;6BACF;yBACF;wBACD,sBAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,EAAA;;;;KAClC;IACH,aAAC;AAAD,CAAC,AAlCD,CAA4B,SAAG,GAkC9B;AAlCY,wBAAM"}

package/dist/blockView.d.ts

@@ -18,25 +18,24 @@ interface Options {
  * @constructs
  */
 export declare class BlockView {
-    private cirTreeOffset;
-    private cirTreeLength;
     private bbi;
-    private isCompressed;
-    private isBigEndian;
     private refsByName;
+    private cirTreeOffset;
+    private isBigEndian;
+    private isCompressed;
     private blockType;
     private cirTreePromise?;
     private featureCache;
     private leafParser;
-    private bigWigParser;
     private bigBedParser;
-    private summaryParser;
-    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, cirTreeLength: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
+    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
     readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts: Options): Promise<void>;
     private parseSummaryBlock;
     private parseBigBedBlock;
     private parseBigWigBlock;
-    private static coordFilter;
-    readFeatures(observer: Observer<Feature[]>, blocks: any, opts?: Options): Promise<void>;
+    readFeatures(observer: Observer<Feature[]>, blocks: {
+        offset: bigint;
+        length: bigint;
+    }[], opts?: Options): Promise<void>;
 }
 export {};