@gmod/bbi 1.0.34 → 2.0.1

package/dist/blockView.js

@@ -51,15 +51,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BlockView = void 0;
-var binary_parser_1 = require("@gmod/binary-parser");
+var binary_parser_1 = require("binary-parser");
 var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
-var unzip_1 = require("./unzip");
 var quick_lru_1 = __importDefault(require("quick-lru"));
+// locals
 var range_1 = __importDefault(require("./range"));
+var unzip_1 = require("./unzip");
 var util_1 = require("./util");
 var BIG_WIG_TYPE_GRAPH = 1;
 var BIG_WIG_TYPE_VSTEP = 2;
 var BIG_WIG_TYPE_FSTEP = 3;
+function coordFilter(s1, e1, s2, e2) {
+    return s1 < e2 && e1 >= s2;
+}
 function getParsers(isBigEndian) {
     var _a;
     var le = isBigEndian ? 'big' : 'little';
@@ -69,10 +73,11 @@ function getParsers(isBigEndian) {
         .uint32('start')
         .uint32('end')
         .uint32('validCnt')
-        .float('minScore')
-        .float('maxScore')
-        .float('sumData')
-        .float('sumSqData');
+        .floatle('minScore')
+        .floatle('maxScore')
+        .floatle('sumData')
+        .floatle('sumSqData')
+        .saveOffset('offset');
     var leafParser = new binary_parser_1.Parser()
         .endianess(le)
         .uint8('isLeaf')
@@ -81,24 +86,28 @@ function getParsers(isBigEndian) {
         .choice({
         tag: 'isLeaf',
         choices: {
-            1: new binary_parser_1.Parser().array('blocksToFetch', {
+            1: new binary_parser_1.Parser().endianess(le).array('blocksToFetch', {
                 length: 'cnt',
                 type: new binary_parser_1.Parser()
+                    .endianess(le)
                     .uint32('startChrom')
                     .uint32('startBase')
                     .uint32('endChrom')
                     .uint32('endBase')
                     .uint64('blockOffset')
-                    .uint64('blockSize'),
+                    .uint64('blockSize')
+                    .saveOffset('offset'),
             }),
             0: new binary_parser_1.Parser().array('recurOffsets', {
                 length: 'cnt',
                 type: new binary_parser_1.Parser()
+                    .endianess(le)
                     .uint32('startChrom')
                     .uint32('startBase')
                     .uint32('endChrom')
                     .uint32('endBase')
-                    .uint64('blockOffset'),
+                    .uint64('blockOffset')
+                    .saveOffset('offset'),
             }),
         },
     });
@@ -109,7 +118,8 @@ function getParsers(isBigEndian) {
         .int32('end')
         .string('rest', {
         zeroTerminated: true,
-    });
+    })
+        .saveOffset('offset');
     var bigWigParser = new binary_parser_1.Parser()
         .endianess(le)
         .skip(4)
@@ -125,15 +135,19 @@ function getParsers(isBigEndian) {
         choices: (_a = {},
             _a[BIG_WIG_TYPE_FSTEP] = new binary_parser_1.Parser().array('items', {
                 length: 'itemCount',
-                type: new binary_parser_1.Parser().float('score'),
+                type: new binary_parser_1.Parser().floatle('score'),
             }),
             _a[BIG_WIG_TYPE_VSTEP] = new binary_parser_1.Parser().array('items', {
                 length: 'itemCount',
-                type: new binary_parser_1.Parser().int32('start').float('score'),
+                type: new binary_parser_1.Parser().endianess(le).int32('start').floatle('score'),
             }),
             _a[BIG_WIG_TYPE_GRAPH] = new binary_parser_1.Parser().array('items', {
                 length: 'itemCount',
-                type: new binary_parser_1.Parser().int32('start').int32('end').float('score'),
+                type: new binary_parser_1.Parser()
+                    .endianess(le)
+                    .int32('start')
+                    .int32('end')
+                    .floatle('score'),
             }),
             _a),
     });
@@ -152,17 +166,26 @@ function getParsers(isBigEndian) {
  * @constructs
  */
 var BlockView = /** @class */ (function () {
-    function BlockView(bbi, refsByName, cirTreeOffset, cirTreeLength, isBigEndian, isCompressed, blockType) {
+    function BlockView(bbi, refsByName, cirTreeOffset, isBigEndian, isCompressed, blockType) {
         var _this = this;
+        this.bbi = bbi;
+        this.refsByName = refsByName;
+        this.cirTreeOffset = cirTreeOffset;
+        this.isBigEndian = isBigEndian;
+        this.isCompressed = isCompressed;
+        this.blockType = blockType;
         this.featureCache = new abortable_promise_cache_1.default({
             cache: new quick_lru_1.default({ maxSize: 1000 }),
             fill: function (requestData, signal) { return __awaiter(_this, void 0, void 0, function () {
-                var length, offset, buffer;
+                var len, off, buffer;
                 return __generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
-                            length = requestData.length, offset = requestData.offset;
-                            return [4 /*yield*/, this.bbi.read(Buffer.alloc(length), 0, length, offset, { signal: signal })];
+                            len = Number(requestData.length);
+                            off = Number(requestData.offset);
+                            return [4 /*yield*/, this.bbi.read(Buffer.alloc(len), 0, len, off, {
+                                    signal: signal,
+                                })];
                         case 1:
                             buffer = (_a.sent()).buffer;
                             return [2 /*return*/, buffer];
@@ -173,37 +196,27 @@ var BlockView = /** @class */ (function () {
         if (!(cirTreeOffset >= 0)) {
             throw new Error('invalid cirTreeOffset!');
         }
-        if (!(cirTreeLength > 0)) {
-            throw new Error('invalid cirTreeLength!');
-        }
-        this.cirTreeOffset = cirTreeOffset;
-        this.cirTreeLength = cirTreeLength;
-        this.isCompressed = isCompressed;
-        this.refsByName = refsByName;
-        this.isBigEndian = isBigEndian;
-        this.bbi = bbi;
-        this.blockType = blockType;
-        Object.assign(this, getParsers(isBigEndian));
+        var parsers = getParsers(isBigEndian);
+        this.leafParser = parsers.leafParser;
+        this.bigBedParser = parsers.bigBedParser;
     }
     BlockView.prototype.readWigData = function (chrName, start, end, observer, opts) {
         return __awaiter(this, void 0, void 0, function () {
-            var _a, refsByName, bbi, cirTreeOffset, isBigEndian, signal_1, chrId_1, request_1, 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, off, 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) {
                     case 0:
                         _b.trys.push([0, 2, , 3]);
                         _a = this, refsByName = _a.refsByName, bbi = _a.bbi, cirTreeOffset = _a.cirTreeOffset, isBigEndian = _a.isBigEndian;
-                        signal_1 = opts.signal;
                         chrId_1 = refsByName[chrName];
                         if (chrId_1 === undefined) {
                             observer.complete();
                         }
                         request_1 = { chrId: chrId_1, start: start, end: end };
                         if (!this.cirTreePromise) {
-                            this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, cirTreeOffset, {
-                                signal: signal_1,
-                            });
+                            off = Number(cirTreeOffset);
+                            this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, off, opts);
                         }
                         return [4 /*yield*/, this.cirTreePromise];
                     case 1:
@@ -215,10 +228,12 @@ var BlockView = /** @class */ (function () {
                         outstanding_1 = 0;
                         cirFobRecur2_1 = function (cirBlockData, offset, level) {
                             try {
-                                var data = cirBlockData.slice(offset);
-                                var p = _this.leafParser.parse(data).result;
+                                var data = cirBlockData.subarray(offset);
+                                var p = _this.leafParser.parse(data);
                                 if (p.blocksToFetch) {
-                                    blocksToFetch_1 = blocksToFetch_1.concat(p.blocksToFetch.filter(filterFeats_1).map(function (l) { return ({
+                                    blocksToFetch_1 = blocksToFetch_1.concat(p.blocksToFetch
+                                        .filter(filterFeats_1)
+                                        .map(function (l) { return ({
                                         offset: l.blockOffset,
                                         length: l.blockSize,
                                     }); }));
@@ -226,7 +241,7 @@ var BlockView = /** @class */ (function () {
                                 if (p.recurOffsets) {
                                     var recurOffsets = p.recurOffsets
                                         .filter(filterFeats_1)
-                                        .map(function (l) { return l.blockOffset; });
+                                        .map(function (l) { return Number(l.blockOffset); });
                                     if (recurOffsets.length > 0) {
                                         cirFobRecur_1(recurOffsets, level + 1);
                                     }
@@ -249,7 +264,7 @@ var BlockView = /** @class */ (function () {
                                         _a.trys.push([0, 2, , 3]);
                                         length_1 = fr.max() - fr.min();
                                         offset = fr.min();
-                                        return [4 /*yield*/, this.featureCache.get("".concat(length_1, "_").concat(offset), { length: length_1, offset: offset }, signal_1)];
+                                        return [4 /*yield*/, this.featureCache.get("".concat(length_1, "_").concat(offset), { length: length_1, offset: offset }, opts.signal)];
                                     case 1:
                                         resultBuffer = _a.sent();
                                         for (i = 0; i < off.length; i += 1) {
@@ -273,7 +288,7 @@ var BlockView = /** @class */ (function () {
                         cirFobRecur_1 = function (offset, level) {
                             try {
                                 outstanding_1 += offset.length;
-                                var maxCirBlockSpan = 4 + cirBlockSize_1 * 32; // Upper bound on size, based on a completely full leaf node.
+                                var maxCirBlockSpan = 4 + Number(cirBlockSize_1) * 32; // Upper bound on size, based on a completely full leaf node.
                                 var spans = new range_1.default(offset[0], offset[0] + maxCirBlockSpan);
                                 for (var i = 1; i < offset.length; i += 1) {
                                     var blockSpan = new range_1.default(offset[i], offset[i] + maxCirBlockSpan);
@@ -285,7 +300,7 @@ var BlockView = /** @class */ (function () {
                                 observer.error(e);
                             }
                         };
-                        return [2 /*return*/, cirFobRecur_1([cirTreeOffset + 48], 1)];
+                        return [2 /*return*/, cirFobRecur_1([Number(cirTreeOffset) + 48], 1)];
                     case 2:
                         e_1 = _b.sent();
                         observer.error(e_1);
@@ -295,98 +310,145 @@ var BlockView = /** @class */ (function () {
             });
         });
     };
-    BlockView.prototype.parseSummaryBlock = function (data, startOffset, request) {
+    BlockView.prototype.parseSummaryBlock = function (buffer, startOffset, request) {
         var features = [];
-        var currOffset = startOffset;
-        while (currOffset < data.byteLength) {
-            var res = this.summaryParser.parse(data.slice(currOffset));
-            features.push(res.result);
-            currOffset += res.offset;
-        }
-        var items = features;
-        if (request) {
-            items = items.filter(function (elt) { return elt.chromId === request.chrId; });
+        var offset = startOffset;
+        var dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
+        while (offset < buffer.byteLength) {
+            // this was extracted from looking at the runtime code generated by
+            // binary-parser
+            var chromId = dataView.getUint32(offset, true);
+            offset += 4;
+            var start = dataView.getUint32(offset, true);
+            offset += 4;
+            var end = dataView.getUint32(offset, true);
+            offset += 4;
+            var validCnt = dataView.getUint32(offset, true);
+            offset += 4;
+            var minScore = dataView.getFloat32(offset, true);
+            offset += 4;
+            var maxScore = dataView.getFloat32(offset, true);
+            offset += 4;
+            var sumData = dataView.getFloat32(offset, true);
+            offset += 4;
+            // unused
+            // const sumSqData = dataView.getFloat32(offset, true)
+            offset += 4;
+            if (request
+                ? chromId === request.chrId &&
+                    coordFilter(start, end, request.start, request.end)
+                : true) {
+                features.push({
+                    start: start,
+                    end: end,
+                    maxScore: maxScore,
+                    minScore: minScore,
+                    summary: true,
+                    score: sumData / (validCnt || 1),
+                });
+            }
         }
-        var feats = items.map(function (elt) { return ({
-            start: elt.start,
-            end: elt.end,
-            maxScore: elt.maxScore,
-            minScore: elt.minScore,
-            score: elt.sumData / (elt.validCnt || 1),
-            summary: true,
-        }); });
-        return request
-            ? feats.filter(function (f) { return BlockView.coordFilter(f, request); })
-            : feats;
+        return features;
     };
     BlockView.prototype.parseBigBedBlock = function (data, startOffset, offset, request) {
         var items = [];
         var currOffset = startOffset;
         while (currOffset < data.byteLength) {
-            var res = this.bigBedParser.parse(data.slice(currOffset));
-            res.result.uniqueId = "bb-".concat(offset + currOffset);
-            items.push(res.result);
+            var res = this.bigBedParser.parse(data.subarray(currOffset));
+            items.push(__assign(__assign({}, res), { uniqueId: "bb-".concat(offset + currOffset) }));
             currOffset += res.offset;
         }
         return request
-            ? items.filter(function (f) { return BlockView.coordFilter(f, request); })
+            ? items.filter(function (f) {
+                return coordFilter(f.start, f.end, request.start, request.end);
+            })
             : items;
     };
-    BlockView.prototype.parseBigWigBlock = function (bytes, startOffset, request) {
-        var data = bytes.slice(startOffset);
-        var results = this.bigWigParser.parse(data).result;
-        var items = results.items, itemSpan = results.itemSpan, itemStep = results.itemStep, blockStart = results.blockStart, blockType = results.blockType;
-        if (blockType === BIG_WIG_TYPE_FSTEP) {
-            for (var i = 0; i < items.length; i++) {
-                items[i].start = blockStart + i * itemStep;
-                items[i].end = blockStart + i * itemStep + itemSpan;
-            }
-        }
-        else if (blockType === BIG_WIG_TYPE_VSTEP) {
-            for (var i = 0; i < items.length; i++) {
-                items[i].end = items[i].start + itemSpan;
-            }
+    BlockView.prototype.parseBigWigBlock = function (buffer, startOffset, request) {
+        var b = buffer.subarray(startOffset);
+        var dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        var offset = 0;
+        offset += 4;
+        var blockStart = dataView.getInt32(offset, true);
+        offset += 8;
+        var itemStep = dataView.getUint32(offset, true);
+        offset += 4;
+        var itemSpan = dataView.getUint32(offset, true);
+        offset += 4;
+        var blockType = dataView.getUint8(offset);
+        offset += 2;
+        var itemCount = dataView.getUint16(offset, true);
+        offset += 2;
+        var items = new Array(itemCount);
+        switch (blockType) {
+            case 1:
+                for (var i = 0; i < itemCount; i++) {
+                    var start = dataView.getInt32(offset, true);
+                    offset += 4;
+                    var end = dataView.getInt32(offset, true);
+                    offset += 4;
+                    var score = dataView.getFloat32(offset, true);
+                    offset += 4;
+                    items[i] = { start: start, end: end, score: score };
+                }
+                break;
+            case 2:
+                for (var i = 0; i < itemCount; i++) {
+                    var start = dataView.getInt32(offset, true);
+                    offset += 4;
+                    var score = dataView.getFloat32(offset, true);
+                    offset += 4;
+                    items[i] = { score: score, start: start, end: start + itemSpan };
+                }
+                break;
+            case 3:
+                for (var i = 0; i < itemCount; i++) {
+                    var score = dataView.getFloat32(offset, true);
+                    offset += 4;
+                    var start = blockStart + i * itemStep;
+                    items[i] = { score: score, start: start, end: start + itemSpan };
+                }
+                break;
         }
         return request
-            ? items.filter(function (f) { return BlockView.coordFilter(f, request); })
+            ? items.filter(function (f) {
+                return coordFilter(f.start, f.end, request.start, request.end);
+            })
             : items;
     };
-    BlockView.coordFilter = function (f, range) {
-        return f.start < range.end && f.end >= range.start;
-    };
     BlockView.prototype.readFeatures = function (observer, blocks, opts) {
         if (opts === void 0) { opts = {}; }
         return __awaiter(this, void 0, void 0, function () {
-            var _a, blockType_1, isCompressed_1, signal_2, request_2, blockGroupsToFetch, e_3;
+            var _a, blockType_1, isCompressed_1, signal_1, request_2, blockGroupsToFetch, e_3;
             var _this = this;
             return __generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         _b.trys.push([0, 2, , 3]);
                         _a = this, blockType_1 = _a.blockType, isCompressed_1 = _a.isCompressed;
-                        signal_2 = opts.signal, request_2 = opts.request;
+                        signal_1 = opts.signal, request_2 = opts.request;
                         blockGroupsToFetch = (0, util_1.groupBlocks)(blocks);
-                        (0, util_1.checkAbortSignal)(signal_2);
+                        (0, util_1.checkAbortSignal)(signal_1);
                         return [4 /*yield*/, Promise.all(blockGroupsToFetch.map(function (blockGroup) { return __awaiter(_this, void 0, void 0, function () {
                                 var length, offset, data;
                                 var _this = this;
                                 return __generator(this, function (_a) {
                                     switch (_a.label) {
                                         case 0:
-                                            (0, util_1.checkAbortSignal)(signal_2);
+                                            (0, util_1.checkAbortSignal)(signal_1);
                                             length = blockGroup.length, offset = blockGroup.offset;
-                                            return [4 /*yield*/, this.featureCache.get("".concat(length, "_").concat(offset), blockGroup, signal_2)];
+                                            return [4 /*yield*/, this.featureCache.get("".concat(length, "_").concat(offset), blockGroup, signal_1)];
                                         case 1:
                                             data = _a.sent();
                                             blockGroup.blocks.forEach(function (block) {
-                                                (0, util_1.checkAbortSignal)(signal_2);
-                                                var blockOffset = block.offset - blockGroup.offset;
+                                                (0, util_1.checkAbortSignal)(signal_1);
+                                                var blockOffset = Number(block.offset) - Number(blockGroup.offset);
                                                 var resultData = data;
                                                 if (isCompressed_1) {
-                                                    resultData = (0, unzip_1.unzip)(data.slice(blockOffset));
+                                                    resultData = (0, unzip_1.unzip)(data.subarray(blockOffset));
                                                     blockOffset = 0;
                                                 }
-                                                (0, util_1.checkAbortSignal)(signal_2);
+                                                (0, util_1.checkAbortSignal)(signal_1);
                                                 switch (blockType_1) {
                                                     case 'summary':
                                                         observer.next(_this.parseSummaryBlock(resultData, blockOffset, request_2));
@@ -395,9 +457,7 @@ var BlockView = /** @class */ (function () {
                                                         observer.next(_this.parseBigWigBlock(resultData, blockOffset, request_2));
                                                         break;
                                                     case 'bigbed':
-                                                        observer.next(_this.parseBigBedBlock(resultData, blockOffset, 
-                                                        // eslint-disable-next-line no-bitwise
-                                                        block.offset * (1 << 8), request_2));
+                                                        observer.next(_this.parseBigBedBlock(resultData, blockOffset, Number(block.offset) * (1 << 8), request_2));
                                                         break;
                                                     default:
                                                         console.warn("Don't know what to do with ".concat(blockType_1));
@@ -423,3 +483,4 @@ var BlockView = /** @class */ (function () {
     return BlockView;
 }());
 exports.BlockView = BlockView;
+//# sourceMappingURL=blockView.js.map

package/dist/blockView.js.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -5,3 +5,4 @@ var bigwig_1 = require("./bigwig");
 Object.defineProperty(exports, "BigWig", { enumerable: true, get: function () { return bigwig_1.BigWig; } });
 var bigbed_1 = require("./bigbed");
 Object.defineProperty(exports, "BigBed", { enumerable: true, get: function () { return bigbed_1.BigBed; } });
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +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"}

package/dist/range.js

@@ -106,6 +106,7 @@ var Range = /** @class */ (function () {
         var b = tmpb;
         if (arguments.length < 2) {
             b = a;
+            // eslint-disable-next-line @typescript-eslint/no-this-alias
             a = this;
         }
         if (a.min() < b.min()) {
@@ -125,3 +126,4 @@ var Range = /** @class */ (function () {
     return Range;
 }());
 exports.default = Range;
+//# sourceMappingURL=range.js.map

package/dist/range.js.map

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

@@ -1,2 +1,2 @@
 /// <reference types="node" />
-export declare function unzip(input: Buffer): Buffer;
+export declare function unzip(input: Buffer): Uint8Array;

package/dist/unzip-pako.js

@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.unzip = void 0;
 var pako_1 = require("pako");
 function unzip(input) {
-    return Buffer.from((0, pako_1.inflate)(input));
+    return (0, pako_1.inflateRaw)(input.subarray(2));
 }
 exports.unzip = unzip;
+//# sourceMappingURL=unzip-pako.js.map

package/dist/unzip-pako.js.map

@@ -0,0 +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"}

package/dist/unzip.js

@@ -3,3 +3,4 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.unzip = void 0;
 var 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

@@ -0,0 +1 @@
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAAkC;AACV,sFADf,kBAAW,OACS"}

package/dist/util.d.ts

@@ -2,7 +2,17 @@ export declare class AbortError extends Error {
     code: string;
     constructor(message: string);
 }
-export declare function groupBlocks(blocks: any[]): any[];
+export declare function groupBlocks(blocks: {
+    offset: bigint;
+    length: bigint;
+}[]): {
+    blocks: {
+        offset: bigint;
+        length: bigint;
+    }[];
+    length: bigint;
+    offset: bigint;
+}[];
 /**
  * Properly check if the given AbortSignal is aborted.
  * Per the standard, if the signal reads as aborted,

package/dist/util.js

@@ -66,13 +66,18 @@ 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 (b0.offset | 0) - (b1.offset | 0); });
+    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) {
-        if (lastBlock && blocks[i].offset - lastBlockEnd <= 2000) {
-            lastBlock.length += blocks[i].length - lastBlockEnd + blocks[i].offset;
+        if (lastBlock &&
+            lastBlockEnd &&
+            Number(blocks[i].offset) - lastBlockEnd <= 2000) {
+            lastBlock.length = BigInt(Number(lastBlock.length) +
+                Number(blocks[i].length) -
+                lastBlockEnd +
+                Number(blocks[i].offset));
             lastBlock.blocks.push(blocks[i]);
         }
         else {
@@ -82,7 +87,7 @@ function groupBlocks(blocks) {
                 offset: blocks[i].offset,
             }));
         }
-        lastBlockEnd = lastBlock.offset + lastBlock.length;
+        lastBlockEnd = Number(lastBlock.offset) + Number(lastBlock.length);
     }
     return blockGroups;
 }
@@ -135,3 +140,4 @@ function abortBreakPoint(signal) {
     });
 }
 exports.abortBreakPoint = abortBreakPoint;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
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package/esm/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;