@gmod/tabix 1.5.4 → 1.5.6

package/dist/util.js

@@ -1,19 +1,4 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
     function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
     return new (P || (P = Promise))(function (resolve, reject) {
@@ -23,33 +8,6 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.optimizeChunks = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = void 0;
 function longToNumber(long) {
@@ -60,13 +18,8 @@ function longToNumber(long) {
     return long.toNumber();
 }
 exports.longToNumber = longToNumber;
-var AbortError = /** @class */ (function (_super) {
-    __extends(AbortError, _super);
-    function AbortError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return AbortError;
-}(Error));
+class AbortError extends Error {
+}
 /**
  * Properly check if the given AbortSignal is aborted.
  * Per the standard, if the signal reads as aborted,
@@ -89,7 +42,7 @@ function checkAbortSignal(signal) {
             throw new DOMException('aborted', 'AbortError');
         }
         else {
-            var e = new AbortError('aborted');
+            const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';
             throw e;
         }
@@ -103,16 +56,9 @@ exports.checkAbortSignal = checkAbortSignal;
  * @param {AbortSignal} signal
  */
 function abortBreakPoint(signal) {
-    return __awaiter(this, void 0, void 0, function () {
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, Promise.resolve()];
-                case 1:
-                    _a.sent();
-                    checkAbortSignal(signal);
-                    return [2 /*return*/];
-            }
-        });
+    return __awaiter(this, void 0, void 0, function* () {
+        yield Promise.resolve();
+        checkAbortSignal(signal);
     });
 }
 exports.abortBreakPoint = abortBreakPoint;
@@ -122,13 +68,13 @@ function canMergeBlocks(chunk1, chunk2) {
 }
 exports.canMergeBlocks = canMergeBlocks;
 function optimizeChunks(chunks, lowest) {
-    var mergedChunks = [];
-    var lastChunk = null;
+    const mergedChunks = [];
+    let lastChunk = null;
     if (chunks.length === 0) {
         return chunks;
     }
     chunks.sort(function (c0, c1) {
-        var dif = c0.minv.blockPosition - c1.minv.blockPosition;
+        const dif = c0.minv.blockPosition - c1.minv.blockPosition;
         if (dif !== 0) {
             return dif;
         }
@@ -136,7 +82,7 @@ function optimizeChunks(chunks, lowest) {
             return c0.minv.dataPosition - c1.minv.dataPosition;
         }
     });
-    chunks.forEach(function (chunk) {
+    chunks.forEach(chunk => {
         if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
             if (lastChunk === null) {
                 mergedChunks.push(chunk);

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;AAGA,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC;QACA,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;KACpC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AARD,oCAQC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE;QACX,OAAM;KACP;IAED,IAAI,MAAM,CAAC,OAAO,EAAE;QAClB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE;YACvC,qCAAqC;YACrC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;SAChD;aAAM;YACL,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;SACR;KACF;AACH,CAAC;AAhBD,4CAgBC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAHD,0CAGC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AALD,wCAKC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAqB;IACnE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAiB,IAAI,CAAA;IAElC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,OAAO,MAAM,CAAA;KACd;IAED,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,EAAE,EAAE;QAC1B,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,IAAI,GAAG,KAAK,CAAC,EAAE;YACb,OAAO,GAAG,CAAA;SACX;aAAM;YACL,OAAO,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;SACnD;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACrB,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;YAC/C,IAAI,SAAS,KAAK,IAAI,EAAE;gBACtB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;aAClB;iBAAM;gBACL,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE;oBACpC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE;wBAC5C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;qBAC5B;iBACF;qBAAM;oBACL,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;iBAClB;aACF;SACF;QACD,SAAS;QACT,2CAA2C;QAC3C,IAAI;IACN,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC;AAvCD,wCAuCC"}

package/dist/virtualOffset.js

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

package/dist/virtualOffset.js.map

@@ -1 +1 @@
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+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AAAA,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE;YACnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;SACd;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;gBAC9B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;aACd;SACF;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;KACnE;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}

package/esm/tabixIndexedFile.d.ts

@@ -2,7 +2,7 @@
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options } from './indexFile';
 import Chunk from './chunk';
-declare type GetLinesCallback = (line: string, fileOffset: number) => void;
+type GetLinesCallback = (line: string, fileOffset: number) => void;
 interface GetLinesOpts {
     [key: string]: unknown;
     signal?: AbortSignal;

package/esm/tabixIndexedFile.js

@@ -5,6 +5,7 @@ import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
 import { checkAbortSignal } from './util';
 import TBI from './tbi';
 import CSI from './csi';
+const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined;
 function timeout(time) {
     return new Promise(resolve => {
         setTimeout(resolve, time);
@@ -135,19 +136,24 @@ export default class TabixIndexedFile {
             let previousStartCoordinate;
             const c = chunks[chunkNum];
             const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
-            const lines = (typeof TextDecoder !== 'undefined'
-                ? new TextDecoder('utf-8').decode(buffer)
-                : buffer.toString()).split('\n');
-            lines.pop();
             checkAbortSignal(signal);
-            let blockStart = c.minv.dataPosition;
-            let pos;
-            for (let i = 0; i < lines.length; i += 1) {
-                const line = lines[i];
-                for (pos = 0; blockStart >= dpositions[pos]; pos += 1) { }
+            let blockStart = 0;
+            let pos = 0;
+            while (blockStart < buffer.length) {
+                const n = buffer.indexOf('\n', blockStart);
+                if (n === -1) {
+                    break;
+                }
+                const b = buffer.subarray(blockStart, n);
+                const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
+                if (dpositions) {
+                    while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
+                    pos--;
+                }
                 // filter the line for whether it is within the requested range
                 const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
-                // do a small check just to make sure that the lines are really sorted by start coordinate
+                // do a small check just to make sure that the lines are really sorted
+                // by start coordinate
                 if (previousStartCoordinate !== undefined &&
                     startCoordinate !== undefined &&
                     previousStartCoordinate > startCoordinate) {
@@ -164,7 +170,10 @@ export default class TabixIndexedFile {
                     // then the blockStart-dpositions is an uncompressed file offset from
                     // that bgzip block boundary, and since the cpositions are multiplied by
                     // (1 << 8) these uncompressed offsets get a unique space
-                    cpositions[pos] * (1 << 8) + (blockStart - dpositions[pos]));
+                    cpositions[pos] * (1 << 8) +
+                        (blockStart - dpositions[pos]) +
+                        c.minv.dataPosition +
+                        1);
                 }
                 else if (startCoordinate !== undefined && startCoordinate >= end) {
                     // the lines were overlapping the region, but now have stopped, so
@@ -172,13 +181,13 @@ export default class TabixIndexedFile {
                     // processing data now
                     return;
                 }
-                blockStart += line.length + 1;
                 // yield if we have emitted beyond the yield limit
                 if (last - Date.now() > 500) {
                     last = Date.now();
                     checkAbortSignal(signal);
                     await timeout(1);
                 }
+                blockStart = n + 1;
             }
         }
     }

package/esm/tabixIndexedFile.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.4",
+  "version": "1.5.6",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -26,7 +26,7 @@
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean && npm run lint",
     "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es5 --outDir dist",
+    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "preversion": "npm run lint && npm test && npm run build",
     "prepublishOnly": "npm run lint && npm test && npm run build",
@@ -41,13 +41,12 @@
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.3.3",
     "abortable-promise-cache": "^1.4.1",
-    "es6-promisify": "^6.0.1",
     "generic-filehandle": "^3.0.0",
     "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^28.1.6",
+    "@types/jest": "^29.2.4",
     "@types/long": "^4.0.0",
     "@types/node": "^18.0.6",
     "@types/quick-lru": "2.0.0",
@@ -57,12 +56,12 @@
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
     "eslint-plugin-prettier": "^4.2.1",
-    "jest": "^28.1.3",
-    "jest-environment-jsdom": "^28.1.3",
+    "jest": "^29.3.1",
+    "jest-environment-jsdom": "^29.3.1",
     "prettier": "^2.7.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.27",
-    "ts-jest": "^28.0.7",
+    "ts-jest": "^29.0.3",
     "typescript": "^4.7.4"
   },
   "publishConfig": {

package/src/tabixIndexedFile.ts

@@ -11,6 +11,9 @@ import CSI from './csi'
 
 type GetLinesCallback = (line: string, fileOffset: number) => void
 
+const decoder =
+  typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined
+
 interface GetLinesOpts {
   [key: string]: unknown
   signal?: AbortSignal
@@ -188,21 +191,21 @@ export default class TabixIndexedFile {
         signal,
       )
 
-      const lines = (
-        typeof TextDecoder !== 'undefined'
-          ? new TextDecoder('utf-8').decode(buffer)
-          : buffer.toString()
-      ).split('\n')
-      lines.pop()
-
       checkAbortSignal(signal)
-      let blockStart = c.minv.dataPosition
-      let pos
-
-      for (let i = 0; i < lines.length; i += 1) {
-        const line = lines[i]
+      let blockStart = 0
+      let pos = 0
+      while (blockStart < buffer.length) {
+        const n = buffer.indexOf('\n', blockStart)
+        if (n === -1) {
+          break
+        }
+        const b = buffer.subarray(blockStart, n)
+        const line = decoder?.decode(b) || b.toString()
 
-        for (pos = 0; blockStart >= dpositions[pos]; pos += 1) {}
+        if (dpositions) {
+          while (blockStart + c.minv.dataPosition >= dpositions[pos++]) {}
+          pos--
+        }
 
         // filter the line for whether it is within the requested range
         const { startCoordinate, overlaps } = this.checkLine(
@@ -213,7 +216,8 @@ export default class TabixIndexedFile {
           line,
         )
 
-        // do a small check just to make sure that the lines are really sorted by start coordinate
+        // do a small check just to make sure that the lines are really sorted
+        // by start coordinate
         if (
           previousStartCoordinate !== undefined &&
           startCoordinate !== undefined &&
@@ -236,7 +240,10 @@ export default class TabixIndexedFile {
             // then the blockStart-dpositions is an uncompressed file offset from
             // that bgzip block boundary, and since the cpositions are multiplied by
             // (1 << 8) these uncompressed offsets get a unique space
-            cpositions[pos] * (1 << 8) + (blockStart - dpositions[pos]),
+            cpositions[pos] * (1 << 8) +
+              (blockStart - dpositions[pos]) +
+              c.minv.dataPosition +
+              1,
           )
         } else if (startCoordinate !== undefined && startCoordinate >= end) {
           // the lines were overlapping the region, but now have stopped, so
@@ -244,7 +251,6 @@ export default class TabixIndexedFile {
           // processing data now
           return
         }
-        blockStart += line.length + 1
 
         // yield if we have emitted beyond the yield limit
         if (last - Date.now() > 500) {
@@ -252,6 +258,7 @@ export default class TabixIndexedFile {
           checkAbortSignal(signal)
           await timeout(1)
         }
+        blockStart = n + 1
       }
     }
   }