@gmod/tabix 3.0.5 → 3.1.1

package/dist/tabixIndexedFile.js

@@ -10,10 +10,6 @@ const quick_lru_1 = __importDefault(require("quick-lru"));
 const csi_ts_1 = __importDefault(require("./csi.js"));
 const tbi_ts_1 = __importDefault(require("./tbi.js"));
 const util_ts_1 = require("./util.js");
-function isASCII(str) {
-    // eslint-disable-next-line no-control-regex
-    return /^[\u0000-\u007F]*$/.test(str);
-}
 class TabixIndexedFile {
     /**
      * @param {object} args
@@ -42,6 +38,9 @@ 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 quick_lru_1.default({
+            maxSize: 1000,
+        });
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -121,6 +120,12 @@ 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 = {};
@@ -153,60 +158,71 @@ 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;
             }
         }
     }
@@ -231,11 +247,12 @@ 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;
                 }
             }
@@ -317,7 +334,7 @@ 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;
@@ -328,14 +345,12 @@ 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) {
@@ -352,11 +367,11 @@ class TabixIndexedFile {
                         };
                     }
                 }
-                currentColumnStart = i + 1;
-                currentColumnNumber += 1;
-                if (currentColumnNumber > maxColumn) {
+                if (currentColumnNumber === maxColumn) {
                     break;
                 }
+                currentColumnStart = i + 1;
+                currentColumnNumber += 1;
             }
         }
         return {
@@ -373,17 +388,10 @@ 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) {
@@ -408,7 +416,7 @@ class TabixIndexedFile {
      */
     async readChunk(c, opts = {}) {
         const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
-        return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c);
+        return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c, this.cache);
     }
 }
 exports.default = TabixIndexedFile;

package/dist/tabixIndexedFile.js.map

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package/dist/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/dist/tbi.js

@@ -105,7 +105,7 @@ class TabixIndex extends indexFile_ts_1.default {
         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);
@@ -182,28 +182,6 @@ class TabixIndex extends indexFile_ts_1.default {
             lineCount: (0, long_ts_1.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;
@@ -217,7 +195,7 @@ class TabixIndex extends indexFile_ts_1.default {
         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]
@@ -241,15 +219,13 @@ class TabixIndex extends indexFile_ts_1.default {
         // 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 (0, util_ts_1.optimizeChunks)(chunks, lowest);

package/dist/tbi.js.map

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

@@ -23,14 +23,14 @@ 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');
+        }
     }
 }
 /**
@@ -49,17 +49,17 @@ function canMergeBlocks(chunk1, chunk2) {
 }
 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;
             }
@@ -75,7 +75,7 @@ function optimizeChunks(chunks, lowest) {
                 }
             }
         }
-    });
+    }
     return mergedChunks;
 }
 //# 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":";;AAkBA,4CAcC;AAQD,0CAGC;AAED,wCAKC;AAED,wCAgCC;AAjFD,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;;GAWG;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,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACI,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;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,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,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,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,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;IAED,OAAO,YAAY,CAAA;AACrB,CAAC"}

package/esm/chunk.d.ts

@@ -4,7 +4,7 @@ export default class Chunk {
     maxv: VirtualOffset;
     bin: number;
     _fetchedSize?: number;
-    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
+    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: number);
     toUniqueString(): string;
     toString(): string;
     compareTo(b: Chunk): number;

package/esm/chunk.js

@@ -1,6 +1,6 @@
 // little class representing a chunk in the index
 export default class Chunk {
-    constructor(minv, maxv, bin, fetchedSize = undefined) {
+    constructor(minv, maxv, bin, fetchedSize) {
         this.minv = minv;
         this.maxv = maxv;
         this.bin = bin;

package/esm/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAoB;QAEpB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}

package/esm/csi.d.ts

@@ -12,7 +12,7 @@ export default class CSI extends IndexFile {
         refIdToName: string[];
         refNameToId: Record<string, number>;
         skipLines: number;
-        metaChar: string | null;
+        metaChar: string | undefined;
         columnNumbers: {
             ref: number;
             start: number;
@@ -21,10 +21,6 @@ export default class CSI extends IndexFile {
         format: string;
         coordinateType: string;
     };
-    _parseNameBytes(namesBytes: Uint8Array): {
-        refNameToId: Record<string, number>;
-        refIdToName: string[];
-    };
     _parse(opts?: Options): Promise<{
         csi: boolean;
         refCount: number;
@@ -43,7 +39,7 @@ export default class CSI extends IndexFile {
         refIdToName: string[];
         refNameToId: Record<string, number>;
         skipLines: number;
-        metaChar: string | null;
+        metaChar: string | undefined;
         columnNumbers: {
             ref: number;
             start: number;
@@ -68,7 +64,7 @@ export default class CSI extends IndexFile {
         maxRefLength: number;
         refIdToName: never[];
         refNameToId: {};
-        metaChar: null;
+        metaChar: undefined;
         columnNumbers: {
             ref: number;
             start: number;

package/esm/csi.js

@@ -57,7 +57,7 @@ export default class CSI extends IndexFile {
             end: dataView.getInt32(offset + 12, true),
         };
         const metaValue = dataView.getInt32(offset + 16, true);
-        const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
+        const metaChar = metaValue ? String.fromCharCode(metaValue) : undefined;
         const skipLines = dataView.getInt32(offset + 20, true);
         const nameSectionLength = dataView.getInt32(offset + 24, true);
         const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
@@ -71,29 +71,6 @@ export default class CSI extends IndexFile {
             coordinateType,
         };
     }
-    _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,
-        };
-    }
-    // fetch and parse the index
     async _parse(opts = {}) {
         const bytes = await unzip(await this.filehandle.readFile(opts));
         const dataView = new DataView(bytes.buffer);
@@ -118,7 +95,7 @@ export default class CSI extends IndexFile {
             : {
                 refIdToName: [],
                 refNameToId: {},
-                metaChar: null,
+                metaChar: undefined,
                 columnNumbers: { ref: 0, start: 1, end: 2 },
                 coordinateType: 'zero-based-half-open',
                 format: 'generic',

package/esm/csi.js.map

@@ -1 +1 @@
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