@gmod/tabix 1.5.13 → 1.5.14

package/CHANGELOG.md

@@ -1,12 +1,19 @@
-## [1.5.13](https://github.com/GMOD/tabix-js/compare/v1.5.12...v1.5.13) (2024-01-09)
+## [1.5.14](https://github.com/GMOD/tabix-js/compare/v1.5.13...v1.5.14) (2024-07-23)
+
+
+### Reverts
 
+* Revert "Bump to eslint 9" ([9bd49b1](https://github.com/GMOD/tabix-js/commit/9bd49b1132f632b0e7847d9b95cf3cb08c424360))
 
 
+
+## [1.5.13](https://github.com/GMOD/tabix-js/compare/v1.5.12...v1.5.13) (2024-01-09)
+
 - Another fix for abort signal in getLines
 
 ## [1.5.12](https://github.com/GMOD/tabix-js/compare/v1.5.11...v1.5.12) (2024-01-09)
 
-- Add missing abort signal to the abortable-promise-cache fetch for tabix chunks
+- Add missing abort signal to the @gmod/abortable-promise-cache fetch for tabix chunks
   (#143)
 
 ## [1.5.11](https://github.com/GMOD/tabix-js/compare/v1.5.10...v1.5.11) (2023-07-10)

package/dist/csi.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';

package/dist/csi.js

@@ -56,8 +56,8 @@ class CSI extends indexFile_1.default {
         this.depth = 0;
         this.minShift = 0;
     }
-    lineCount(refName, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    lineCount(refName_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
             const indexData = yield this.parse(opts);
             if (!indexData) {
                 return -1;
@@ -124,8 +124,8 @@ class CSI extends indexFile_1.default {
         return { refNameToId, refIdToName };
     }
     // fetch and parse the index
-    _parse(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _parse() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const bytes = yield (0, bgzf_filehandle_1.unzip)(yield this.filehandle.readFile(opts));
             // check TBI magic numbers
             let csiVersion;
@@ -199,8 +199,8 @@ class CSI extends indexFile_1.default {
         const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
         return { lineCount };
     }
-    blocksForRange(refName, min, max, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    blocksForRange(refName_1, min_1, max_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, min, max, opts = {}) {
             if (min < 0) {
                 min = 0;
             }

package/dist/csi.js.map

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

@@ -25,8 +25,8 @@ class IndexFile {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeqs;
     }
-    getMetadata(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getMetadata() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const _a = yield this.parse(opts), { indices: _indices } = _a, rest = __rest(_a, ["indices"]);
             return rest;
         });
@@ -41,8 +41,8 @@ class IndexFile {
             return virtualOffset;
         }
     }
-    parse(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    parse() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             if (!this.parseP) {
                 this.parseP = this._parse(opts).catch(e => {
                     this.parseP = undefined;
@@ -52,9 +52,9 @@ class IndexFile {
             return this.parseP;
         });
     }
-    hasRefSeq(seqId, opts = {}) {
-        var _a;
-        return __awaiter(this, void 0, void 0, function* () {
+    hasRefSeq(seqId_1) {
+        return __awaiter(this, arguments, void 0, function* (seqId, opts = {}) {
+            var _a;
             const idx = yield this.parse(opts);
             return !!((_a = idx.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
         });

package/dist/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;AAoBA,MAA8B,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMY,WAAW,CAAC,OAAgB,EAAE;;YACzC,MAAM,KAAiC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAvD,EAAE,OAAO,EAAE,QAAQ,OAAoC,EAA/B,IAAI,cAA5B,WAA8B,CAAyB,CAAA;YAC7D,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAEK,KAAK,CAAC,OAAgB,EAAE;;YAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;gBACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;;YAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAClC,OAAO,CAAC,CAAC,CAAA,MAAA,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;;KACtC;CACF;AA3DD,4BA2DC"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;AAoBA,MAA8B,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMY,WAAW;6DAAC,OAAgB,EAAE;YACzC,MAAM,KAAiC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAvD,EAAE,OAAO,EAAE,QAAQ,OAAoC,EAA/B,IAAI,cAA5B,WAA8B,CAAyB,CAAA;YAC7D,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAEK,KAAK;6DAAC,OAAgB,EAAE;YAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;gBACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS;6DAAC,KAAa,EAAE,OAAgB,EAAE;;YAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAClC,OAAO,CAAC,CAAC,CAAA,MAAA,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;QACvC,CAAC;KAAA;CACF;AA3DD,4BA2DC"}

package/dist/tabixIndexedFile.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options, IndexData } from './indexFile';

package/dist/tabixIndexedFile.js

@@ -12,7 +12,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const buffer_1 = require("buffer");
 const generic_filehandle_1 = require("generic-filehandle");
@@ -97,8 +97,8 @@ class TabixIndexedFile {
      * @returns promise that is resolved when the whole read is finished, rejected on error
      */
     getLines(refName, s, e, opts) {
-        var _a;
         return __awaiter(this, void 0, void 0, function* () {
+            var _a;
             let signal;
             let options = {};
             let callback;
@@ -200,8 +200,8 @@ class TabixIndexedFile {
             }
         });
     }
-    getMetadata(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getMetadata() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             return this.index.getMetadata(opts);
         });
     }
@@ -210,8 +210,8 @@ class TabixIndexedFile {
      * the file, which are the bytes up to the first
      * non-meta line
      */
-    getHeaderBuffer(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getHeaderBuffer() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const { firstDataLine, metaChar, maxBlockSize } = yield this.getMetadata(opts);
             (0, util_1.checkAbortSignal)(opts.signal);
             const maxFetch = ((firstDataLine === null || firstDataLine === void 0 ? void 0 : firstDataLine.blockPosition) || 0) + maxBlockSize;
@@ -244,8 +244,8 @@ class TabixIndexedFile {
      *
      * @returns {Promise} for a string
      */
-    getHeader(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getHeader() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const bytes = yield this.getHeaderBuffer(opts);
             return bytes.toString('utf8');
         });
@@ -255,8 +255,8 @@ class TabixIndexedFile {
      * they occur in the file. reference sequence renaming is not applied
      * to these names.
      */
-    getReferenceSequenceNames(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    getReferenceSequenceNames() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const metadata = yield this.getMetadata(opts);
             return metadata.refIdToName;
         });
@@ -376,13 +376,13 @@ class TabixIndexedFile {
      * @param refSeq reference sequence name
      * @returns number of data lines present on that reference sequence
      */
-    lineCount(refName, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    lineCount(refName_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
             return this.index.lineCount(refName, opts);
         });
     }
-    _readRegion(pos, size, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _readRegion(pos_1, size_1) {
+        return __awaiter(this, arguments, void 0, function* (pos, size, opts = {}) {
             const b = buffer_1.Buffer.alloc(size);
             const { bytesRead, buffer } = yield this.filehandle.read(b, 0, size, pos, opts);
             return buffer.slice(0, bytesRead);
@@ -392,8 +392,8 @@ class TabixIndexedFile {
      * read and uncompress the data in a chunk (composed of one or more
      * contiguous bgzip blocks) of the file
      */
-    readChunk(c, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    readChunk(c_1) {
+        return __awaiter(this, arguments, void 0, function* (c, opts = {}) {
             // fetch the uncompressed data, uncompress carefully a block at a time,
             // and stop when done
             const data = yield this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);

package/dist/tabixIndexedFile.js.map

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

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';

package/dist/tbi.js

@@ -59,8 +59,8 @@ function reg2bins(beg, end) {
     ];
 }
 class TabixIndex extends indexFile_1.default {
-    lineCount(refName, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    lineCount(refName_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
             const indexData = yield this.parse(opts);
             if (!indexData) {
                 return -1;
@@ -78,8 +78,8 @@ class TabixIndex extends indexFile_1.default {
         });
     }
     // fetch and parse the index
-    _parse(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _parse() {
+        return __awaiter(this, arguments, void 0, function* (opts = {}) {
             const buf = yield this.filehandle.readFile(opts);
             const bytes = yield (0, bgzf_filehandle_1.unzip)(buf);
             (0, util_1.checkAbortSignal)(opts.signal);
@@ -202,8 +202,8 @@ class TabixIndex extends indexFile_1.default {
         }
         return { refNameToId, refIdToName };
     }
-    blocksForRange(refName, min, max, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    blocksForRange(refName_1, min_1, max_1) {
+        return __awaiter(this, arguments, void 0, function* (refName, min, max, opts = {}) {
             if (min < 0) {
                 min = 0;
             }

package/dist/tbi.js.map

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

@@ -1,4 +1,3 @@
-/// <reference types="long" />
 import Chunk from './chunk';
 import VirtualOffset from './virtualOffset';
 export declare function longToNumber(long: Long): number;

package/dist/util.js

@@ -9,7 +9,11 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
     });
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.optimizeChunks = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = void 0;
+exports.longToNumber = longToNumber;
+exports.checkAbortSignal = checkAbortSignal;
+exports.abortBreakPoint = abortBreakPoint;
+exports.canMergeBlocks = canMergeBlocks;
+exports.optimizeChunks = optimizeChunks;
 function longToNumber(long) {
     if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
         long.lessThan(Number.MIN_SAFE_INTEGER)) {
@@ -17,7 +21,6 @@ function longToNumber(long) {
     }
     return long.toNumber();
 }
-exports.longToNumber = longToNumber;
 class AbortError extends Error {
 }
 /**
@@ -37,7 +40,6 @@ function checkAbortSignal(signal) {
     }
     if (signal.aborted) {
         if (typeof DOMException !== 'undefined') {
-            // eslint-disable-next-line  no-undef
             throw new DOMException('aborted', 'AbortError');
         }
         else {
@@ -47,7 +49,6 @@ function checkAbortSignal(signal) {
         }
     }
 }
-exports.checkAbortSignal = checkAbortSignal;
 /**
  * Skips to the next tick, then runs `checkAbortSignal`.
  * Await this to inside an otherwise synchronous loop to
@@ -60,12 +61,10 @@ function abortBreakPoint(signal) {
         checkAbortSignal(signal);
     });
 }
-exports.abortBreakPoint = abortBreakPoint;
 function canMergeBlocks(chunk1, chunk2) {
     return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
         chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
 }
-exports.canMergeBlocks = canMergeBlocks;
 function optimizeChunks(chunks, lowest) {
     const mergedChunks = [];
     let lastChunk = null;
@@ -97,5 +96,4 @@ function optimizeChunks(chunks, lowest) {
     });
     return mergedChunks;
 }
-exports.optimizeChunks = optimizeChunks;
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;AAGA,oCAQC;AAgBD,4CAcC;AAQD,0CAGC;AAED,wCAKC;AAED,wCAgCC;AA1FD,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;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;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,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;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,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,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,CAAC;YAChD,IAAI,SAAS,KAAK,IAAI,EAAE,CAAC;gBACvB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC"}

package/dist/virtualOffset.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 export default class VirtualOffset {
     blockPosition: number;

package/dist/virtualOffset.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fromBytes = void 0;
+exports.fromBytes = fromBytes;
 class VirtualOffset {
     constructor(blockPosition, dataPosition) {
         this.blockPosition = blockPosition; // < offset of the compressed data block
@@ -38,5 +38,4 @@ function fromBytes(bytes, offset = 0, bigendian = false) {
         bytes[offset + 3] * 0x100 +
         bytes[offset + 2], (bytes[offset + 1] << 8) | bytes[offset]);
 }
-exports.fromBytes = fromBytes;
 //# sourceMappingURL=virtualOffset.js.map

package/dist/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AACA,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,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;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,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;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"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;AAiCA,8BAcC;AA9CD,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,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;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,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;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"}

package/esm/csi.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';

package/esm/tabixIndexedFile.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
 import { Options, IndexData } from './indexFile';

package/esm/tabixIndexedFile.js

@@ -1,4 +1,4 @@
-import AbortablePromiseCache from 'abortable-promise-cache';
+import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import LRU from 'quick-lru';
 import { Buffer } from 'buffer';
 import { LocalFile } from 'generic-filehandle';

package/esm/tabixIndexedFile.js.map

@@ -1 +1 @@
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package/esm/tbi.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';

package/esm/util.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="long" />
 import Chunk from './chunk';
 import VirtualOffset from './virtualOffset';
 export declare function longToNumber(long: Long): number;

package/esm/util.js

@@ -24,7 +24,6 @@ export function checkAbortSignal(signal) {
     }
     if (signal.aborted) {
         if (typeof DOMException !== 'undefined') {
-            // eslint-disable-next-line  no-undef
             throw new DOMException('aborted', 'AbortError');
         }
         else {

package/esm/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;GAUG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,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;AAED,MAAM,UAAU,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,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;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,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,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,CAAC;YAChD,IAAI,SAAS,KAAK,IAAI,EAAE,CAAC;gBACvB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC"}

package/esm/virtualOffset.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Buffer } from 'buffer';
 export default class VirtualOffset {
     blockPosition: number;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.13",
+  "version": "1.5.14",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -22,7 +22,7 @@
   "scripts": {
     "test": "jest",
     "coverage": "npm test -- --coverage",
-    "lint": "eslint --ext .js,.ts src",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean && npm run lint",
     "build:esm": "tsc --target es2018 --outDir esm",
@@ -39,28 +39,29 @@
     "genomics"
   ],
   "dependencies": {
+    "@gmod/abortable-promise-cache": "^2.0.0",
     "@gmod/bgzf-filehandle": "^1.3.3",
-    "abortable-promise-cache": "^1.4.1",
     "generic-filehandle": "^3.0.0",
     "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^29.5.11",
+    "@eslint/eslintrc": "^3.1.0",
+    "@eslint/js": "^9.7.0",
+    "@types/jest": "^29.5.12",
     "@types/long": "^4.0.0",
-    "@types/node": "^20.10.5",
-    "@typescript-eslint/eslint-plugin": "^6.15.0",
-    "@typescript-eslint/parser": "^6.15.0",
-    "eslint": "^8.40.0",
+    "@types/node": "^20.11.16",
+    "@typescript-eslint/eslint-plugin": "^7.17.0",
+    "@typescript-eslint/parser": "^7.17.0",
+    "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-prettier": "^5.0.1",
-    "eslint-plugin-unicorn": "^49.0.0",
+    "eslint-plugin-unicorn": "^54.0.0",
     "jest": "^29.7.0",
     "jest-environment-jsdom": "^29.5.0",
-    "prettier": "^3.1.1",
-    "rimraf": "^5.0.1",
-    "standard-changelog": "^5.0.0",
+    "prettier": "^3.2.5",
+    "rimraf": "^6.0.1",
+    "standard-changelog": "^6.0.0",
     "ts-jest": "^29.1.1",
     "typescript": "^5.3.3"
   },

package/src/tabixIndexedFile.ts

@@ -1,4 +1,4 @@
-import AbortablePromiseCache from 'abortable-promise-cache'
+import AbortablePromiseCache from '@gmod/abortable-promise-cache'
 import LRU from 'quick-lru'
 import { Buffer } from 'buffer'
 import { GenericFilehandle, LocalFile } from 'generic-filehandle'

package/src/util.ts

@@ -32,7 +32,6 @@ export function checkAbortSignal(signal?: AbortSignal) {
 
   if (signal.aborted) {
     if (typeof DOMException !== 'undefined') {
-      // eslint-disable-next-line  no-undef
       throw new DOMException('aborted', 'AbortError')
     } else {
       const e = new AbortError('aborted')