@gmod/tabix 3.0.5 → 3.1.1

package/esm/indexFile.d.ts

@@ -7,7 +7,7 @@ export interface Options {
 export interface IndexData {
     refNameToId: Record<string, number>;
     refIdToName: string[];
-    metaChar: string | null;
+    metaChar: string | undefined;
     columnNumbers: {
         ref: number;
         start: number;
@@ -31,7 +31,7 @@ export default abstract class IndexFile {
         [key: string]: any;
         refNameToId: Record<string, number>;
         refIdToName: string[];
-        metaChar: string | null;
+        metaChar: string | undefined;
         columnNumbers: {
             ref: number;
             start: number;
@@ -44,4 +44,8 @@ export default abstract class IndexFile {
     _findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
     parse(opts?: Options): Promise<IndexData>;
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
+    _parseNameBytes(namesBytes: Uint8Array): {
+        refNameToId: Record<string, number>;
+        refIdToName: string[];
+    };
 }

package/esm/indexFile.js

@@ -19,9 +19,9 @@ export default class IndexFile {
     }
     async parse(opts = {}) {
         if (!this.parseP) {
-            this.parseP = this._parse(opts).catch((e) => {
+            this.parseP = this._parse(opts).catch((error) => {
                 this.parseP = undefined;
-                throw e;
+                throw error;
             });
         }
         return this.parseP;
@@ -30,5 +30,27 @@ export default class IndexFile {
         const idx = await this.parse(opts);
         return !!idx.indices[seqId]?.binIndex;
     }
+    _parseNameBytes(namesBytes) {
+        let currRefId = 0;
+        let currNameStart = 0;
+        const refIdToName = [];
+        const refNameToId = {};
+        const decoder = new TextDecoder('utf8');
+        for (let i = 0; i < namesBytes.length; i += 1) {
+            if (!namesBytes[i]) {
+                if (currNameStart < i) {
+                    const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
+                    refIdToName[currRefId] = refName;
+                    refNameToId[refName] = currRefId;
+                }
+                currNameStart = i + 1;
+                currRefId += 1;
+            }
+        }
+        return {
+            refNameToId,
+            refIdToName,
+        };
+    }
 }
 //# sourceMappingURL=indexFile.js.map

package/esm/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAmBA,MAAM,CAAC,OAAO,OAAgB,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;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;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;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;gBACvD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,KAAK,CAAA;YACb,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;IAED,eAAe,CAAC,UAAsB;QACpC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAa,EAAE,CAAA;QAChC,MAAM,WAAW,GAA2B,EAAE,CAAA;QAC9C,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;gBACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;oBACtB,MAAM,OAAO,GAAG,IAAI,CAAC,YAAY,CAC/B,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC,CAAC,CACtD,CAAA;oBACD,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBAClC,CAAC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QACD,OAAO;YACL,WAAW;YACX,WAAW;SACZ,CAAA;IACH,CAAC;CACF"}

package/esm/tabixIndexedFile.d.ts

@@ -1,3 +1,4 @@
+import LRU from 'quick-lru';
 import Chunk from './chunk.ts';
 import { IndexData, Options } from './indexFile.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
@@ -12,6 +13,10 @@ export default class TabixIndexedFile {
     private index;
     private renameRefSeq;
     private chunkCache;
+    cache: LRU<string, {
+        buffer: Uint8Array;
+        nextIn: number;
+    }>;
     /**
      * @param {object} args
      *
@@ -64,12 +69,13 @@ export default class TabixIndexedFile {
      * @returns promise that is resolved when the whole read is finished,
      * rejected on error
      */
+    private calculateFileOffset;
     getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
     getMetadata(opts?: Options): Promise<{
         [key: string]: any;
         refNameToId: Record<string, number>;
         refIdToName: string[];
-        metaChar: string | null;
+        metaChar: string | undefined;
         columnNumbers: {
             ref: number;
             start: number;

package/esm/tabixIndexedFile.js

@@ -5,10 +5,6 @@ import LRU from 'quick-lru';
 import CSI from "./csi.js";
 import TBI from "./tbi.js";
 import { checkAbortSignal } from "./util.js";
-function isASCII(str) {
-    // eslint-disable-next-line no-control-regex
-    return /^[\u0000-\u007F]*$/.test(str);
-}
 export default class TabixIndexedFile {
     /**
      * @param {object} args
@@ -37,6 +33,9 @@ export default class TabixIndexedFile {
      * just the names of the reference sequences that are used for querying.
      */
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
+        this.cache = new LRU({
+            maxSize: 1000,
+        });
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -116,6 +115,12 @@ export default class TabixIndexedFile {
      * @returns promise that is resolved when the whole read is finished,
      * rejected on error
      */
+    calculateFileOffset(cpositions, dpositions, pos, blockStart, minvDataPosition) {
+        return (cpositions[pos] * (1 << 8) +
+            (blockStart - dpositions[pos]) +
+            minvDataPosition +
+            1);
+    }
     async getLines(refName, s, e, opts) {
         let signal;
         let options = {};
@@ -148,60 +153,71 @@ export default class TabixIndexedFile {
             let blockStart = 0;
             let pos = 0;
             // fast path, Buffer is just ASCII chars and not gigantor, can be
-            // converted to string and processed directly. if it is not ASCII or
-            // gigantic (chrome max str len is 512Mb), we have to decode line by line
+            // converted to string and processed directly.
+            //
+            // if it is not ASCII or, we have to decode line by line, as it is
+            // otherwise hard to get the right 'fileOffset' based feature IDs
+            //
+            // we use a basic check for isASCII: string length equals buffer length
+            // if it is ASCII...no multi-byte decodings
             const str = decoder.decode(buffer);
-            const strIsASCII = isASCII(str);
-            while (blockStart < str.length) {
-                let line;
-                let n;
-                if (strIsASCII) {
-                    n = str.indexOf('\n', blockStart);
+            const strIsASCII = buffer.length == str.length;
+            if (strIsASCII) {
+                while (blockStart < str.length) {
+                    const n = str.indexOf('\n', blockStart);
                     if (n === -1) {
                         break;
                     }
-                    line = str.slice(blockStart, n);
+                    const line = str.slice(blockStart, n);
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                    if (dpositions) {
+                        const target = blockStart + c.minv.dataPosition;
+                        while (pos < dpositions.length && target >= dpositions[pos]) {
+                            pos++;
+                        }
+                    }
+                    // filter the line for whether it is within the requested range
+                    const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
+                    if (overlaps) {
+                        callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition));
+                    }
+                    else if (startCoordinate !== undefined && startCoordinate >= end) {
+                        // the lines were overlapping the region, but now have stopped, so we
+                        // must be at the end of the relevant data and we can stop processing
+                        // data now
+                        return;
+                    }
+                    blockStart = n + 1;
                 }
-                else {
-                    n = buffer.indexOf('\n'.charCodeAt(0), blockStart);
+            }
+            else {
+                while (blockStart < buffer.length) {
+                    const n = buffer.indexOf('\n'.charCodeAt(0), blockStart);
                     if (n === -1) {
                         break;
                     }
                     const b = buffer.slice(blockStart, n);
-                    line = decoder.decode(b);
-                }
-                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                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);
-                if (overlaps) {
-                    callback(line, 
-                    // cpositions[pos] refers to actual file offset of a bgzip block
-                    // boundaries
-                    //
-                    // we multiply by (1 <<8) in order to make sure each block has a
-                    // "unique" address space so that data in that block could never
-                    // overlap
-                    //
-                    // 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]) +
-                        c.minv.dataPosition +
-                        1);
-                }
-                else if (startCoordinate !== undefined && startCoordinate >= end) {
-                    // the lines were overlapping the region, but now have stopped, so we
-                    // must be at the end of the relevant data and we can stop processing
-                    // data now
-                    return;
+                    const line = decoder.decode(b);
+                    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                    if (dpositions) {
+                        const target = blockStart + c.minv.dataPosition;
+                        while (pos < dpositions.length && target >= dpositions[pos]) {
+                            pos++;
+                        }
+                    }
+                    // filter the line for whether it is within the requested range
+                    const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
+                    if (overlaps) {
+                        callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition));
+                    }
+                    else if (startCoordinate !== undefined && startCoordinate >= end) {
+                        // the lines were overlapping the region, but now have stopped, so we
+                        // must be at the end of the relevant data and we can stop processing
+                        // data now
+                        return;
+                    }
+                    blockStart = n + 1;
                 }
-                blockStart = n + 1;
             }
         }
     }
@@ -226,11 +242,12 @@ export default class TabixIndexedFile {
             let lastNewline = -1;
             const newlineByte = '\n'.charCodeAt(0);
             const metaByte = metaChar.charCodeAt(0);
-            for (let i = 0; i < bytes.length; i += 1) {
-                if (i === lastNewline + 1 && bytes[i] !== metaByte) {
+            for (let i = 0, l = bytes.length; i < l; i++) {
+                const byte = bytes[i];
+                if (i === lastNewline + 1 && byte !== metaByte) {
                     break;
                 }
-                if (bytes[i] === newlineByte) {
+                if (byte === newlineByte) {
                     lastNewline = i;
                 }
             }
@@ -312,7 +329,7 @@ export default class TabixIndexedFile {
                     }
                 }
                 else if (currentColumnNumber === start) {
-                    startCoordinate = parseInt(line.slice(currentColumnStart, i), 10);
+                    startCoordinate = Number.parseInt(line.slice(currentColumnStart, i), 10);
                     // we convert to 0-based-half-open
                     if (coordinateType === '1-based-closed') {
                         startCoordinate -= 1;
@@ -323,14 +340,12 @@ export default class TabixIndexedFile {
                             overlaps: false,
                         };
                     }
-                    if (end === 0 || end === start) {
-                        // if we have no end, we assume the feature is 1 bp long
-                        if (startCoordinate + 1 <= regionStart) {
-                            return {
-                                startCoordinate,
-                                overlaps: false,
-                            };
-                        }
+                    if ((end === 0 || end === start) && // if we have no end, we assume the feature is 1 bp long
+                        startCoordinate + 1 <= regionStart) {
+                        return {
+                            startCoordinate,
+                            overlaps: false,
+                        };
                     }
                 }
                 else if (format === 'VCF' && currentColumnNumber === 4) {
@@ -347,11 +362,11 @@ export default class TabixIndexedFile {
                         };
                     }
                 }
-                currentColumnStart = i + 1;
-                currentColumnNumber += 1;
-                if (currentColumnNumber > maxColumn) {
+                if (currentColumnNumber === maxColumn) {
                     break;
                 }
+                currentColumnStart = i + 1;
+                currentColumnNumber += 1;
             }
         }
         return {
@@ -368,17 +383,10 @@ export default class TabixIndexedFile {
         // be another pairwise feature at the end of this one
         const isTRA = info.includes('SVTYPE=TRA');
         if (info[0] !== '.' && !isTRA) {
-            let prevChar = ';';
-            for (let j = 0; j < info.length; j += 1) {
-                if (prevChar === ';' && info.slice(j, j + 4) === 'END=') {
-                    let valueEnd = info.indexOf(';', j);
-                    if (valueEnd === -1) {
-                        valueEnd = info.length;
-                    }
-                    endCoordinate = parseInt(info.slice(j + 4, valueEnd), 10);
-                    break;
-                }
-                prevChar = info[j];
+            const endRegex = /(?:^|;)END=([^;]+)/;
+            const match = endRegex.exec(info);
+            if (match) {
+                endCoordinate = Number.parseInt(match[1], 10);
             }
         }
         else if (isTRA) {
@@ -403,7 +411,7 @@ export default class TabixIndexedFile {
      */
     async readChunk(c, opts = {}) {
         const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
-        return unzipChunkSlice(ret, c);
+        return unzipChunkSlice(ret, c, this.cache);
     }
 }
 //# sourceMappingURL=tabixIndexedFile.js.map

package/esm/tabixIndexedFile.js.map

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

@@ -11,7 +11,7 @@ export default class TabixIndex extends IndexFile {
                 lineCount: number;
             } | undefined;
         }[];
-        metaChar: string | null;
+        metaChar: string | undefined;
         maxBinNumber: number;
         maxRefLength: number;
         skipLines: number;
@@ -30,9 +30,5 @@ export default class TabixIndex extends IndexFile {
     parsePseudoBin(bytes: Uint8Array, offset: number): {
         lineCount: number;
     };
-    _parseNameBytes(namesBytes: Uint8Array): {
-        refNameToId: Record<string, number>;
-        refIdToName: string[];
-    };
     blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
 }

package/esm/tbi.js

@@ -67,7 +67,7 @@ export default class TabixIndex extends IndexFile {
         const depth = 5;
         const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
         const maxRefLength = 2 ** (14 + depth * 3);
-        const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
+        const metaChar = metaValue ? String.fromCharCode(metaValue) : undefined;
         const skipLines = dataView.getInt32(28, true);
         // read sequence dictionary
         const nameSectionLength = dataView.getInt32(32, true);
@@ -144,28 +144,6 @@ export default class TabixIndex extends IndexFile {
             lineCount: longFromBytesToUnsigned(bytes, offset + 16),
         };
     }
-    _parseNameBytes(namesBytes) {
-        let currRefId = 0;
-        let currNameStart = 0;
-        const refIdToName = [];
-        const refNameToId = {};
-        const decoder = new TextDecoder('utf8');
-        for (let i = 0; i < namesBytes.length; i += 1) {
-            if (!namesBytes[i]) {
-                if (currNameStart < i) {
-                    const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
-                    refIdToName[currRefId] = refName;
-                    refNameToId[refName] = currRefId;
-                }
-                currNameStart = i + 1;
-                currRefId += 1;
-            }
-        }
-        return {
-            refNameToId,
-            refIdToName,
-        };
-    }
     async blocksForRange(refName, min, max, opts = {}) {
         if (min < 0) {
             min = 0;
@@ -179,7 +157,7 @@ export default class TabixIndex extends IndexFile {
         if (!ba) {
             return [];
         }
-        const minOffset = ba.linearIndex.length
+        const minOffset = ba.linearIndex.length > 0
             ? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
                 ? ba.linearIndex.length - 1
                 : min >> TAD_LIDX_SHIFT]
@@ -203,15 +181,13 @@ export default class TabixIndex extends IndexFile {
         // Use the linear index to find minimum file position of chunks that could
         // contain alignments in the region
         const nintv = ba.linearIndex.length;
-        let lowest = null;
+        let lowest;
         const minLin = Math.min(min >> 14, nintv - 1);
         const maxLin = Math.min(max >> 14, nintv - 1);
         for (let i = minLin; i <= maxLin; ++i) {
             const vp = ba.linearIndex[i];
-            if (vp) {
-                if (!lowest || vp.compareTo(lowest) < 0) {
-                    lowest = vp;
-                }
+            if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+                lowest = vp;
             }
         }
         return optimizeChunks(chunks, lowest);

package/esm/tbi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAsB,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AACnD,OAAO,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5D,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAE7D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;IAC/C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACxD,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;QAC9B,gBAAgB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAC7B,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,6CAA6C;QAC7C,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC/C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,UAAU,GAA2B;YACzC,CAAC,EAAE,SAAS;YACZ,CAAC,EAAE,KAAK;YACR,CAAC,EAAE,KAAK;SACT,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAChC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAClC,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;SACjC,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAE7C,2BAA2B;QAC3B,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QACrD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;QAED,+CAA+C;QAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACvC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACpD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;gBAChD,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;oBACtD,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAChD,CAAC;oBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;gBAC/B,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;oBACtD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,mBAAmB;YACnB,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACvD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CA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package/esm/util.js

@@ -17,14 +17,14 @@ export function checkAbortSignal(signal) {
         return;
     }
     if (signal.aborted) {
-        if (typeof DOMException !== 'undefined') {
-            throw new DOMException('aborted', 'AbortError');
-        }
-        else {
+        if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';
             throw e;
         }
+        else {
+            throw new DOMException('aborted', 'AbortError');
+        }
     }
 }
 /**
@@ -43,17 +43,17 @@ export function canMergeBlocks(chunk1, chunk2) {
 }
 export function optimizeChunks(chunks, lowest) {
     const mergedChunks = [];
-    let lastChunk = null;
+    let lastChunk;
     if (chunks.length === 0) {
         return chunks;
     }
     chunks.sort(function (c0, c1) {
         const dif = c0.minv.blockPosition - c1.minv.blockPosition;
-        return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition;
+        return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif;
     });
-    chunks.forEach(chunk => {
+    for (const chunk of chunks) {
         if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-            if (lastChunk === null) {
+            if (lastChunk === undefined) {
                 mergedChunks.push(chunk);
                 lastChunk = chunk;
             }
@@ -69,7 +69,7 @@ export function optimizeChunks(chunks, lowest) {
                 }
             }
         }
-    });
+    }
     return mergedChunks;
 }
 //# sourceMappingURL=util.js.map

package/esm/util.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.0.5",
+  "version": "3.1.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
   "types": "./dist/index.d.ts",
@@ -35,14 +35,14 @@
     "format": "prettier --write .",
     "docs": "documentation readme --shallow src/tabixIndexedFile.ts --section TabixIndexedFile",
     "clean": "rimraf dist esm",
-    "prebuild": "npm run clean && npm run lint",
+    "prebuild": "yarn clean",
     "build:esm": "tsc --target es2020 --outDir esm",
     "build:es5": "tsc --target es2020 --module commonjs --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "build": "npm run build:esm && npm run build:es5",
+    "build": "yarn build:esm && yarn build:es5",
     "postbuild": "webpack",
-    "preversion": "npm run lint && npm test run && npm run build",
-    "prepublishOnly": "npm run lint && npm test run && npm run build",
+    "preversion": "yarn lint && npm test run && yarn build",
+    "prepublishOnly": "yarn lint && npm test run && yarn build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push --follow-tags"
   },
@@ -59,17 +59,17 @@
   },
   "devDependencies": {
     "@types/node": "^22.15.3",
-    "@vitest/coverage-v8": "^3.0.1",
+    "@vitest/coverage-v8": "^4.0.6",
     "documentation": "^14.0.3",
     "eslint": "^9.9.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^59.0.0",
+    "eslint-plugin-unicorn": "^62.0.0",
     "prettier": "^3.3.3",
     "rimraf": "^6.0.1",
     "standard-changelog": "^7.0.1",
     "typescript": "^5.7.0",
     "typescript-eslint": "^8.0.1",
-    "vitest": "^3.0.1",
+    "vitest": "^4.0.6",
     "webpack": "^5.93.0",
     "webpack-cli": "^6.0.1"
   },