@gmod/tabix 1.6.1 → 2.0.0

package/dist/tabixIndexedFile.js

@@ -5,8 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 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");
+const generic_filehandle2_1 = require("generic-filehandle2");
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const util_1 = require("./util");
 const tbi_1 = __importDefault(require("./tbi"));
@@ -15,7 +14,6 @@ function isASCII(str) {
     // eslint-disable-next-line no-control-regex
     return /^[\u0000-\u007F]*$/.test(str);
 }
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 class TabixIndexedFile {
     /**
      * @param {object} args
@@ -48,10 +46,10 @@ class TabixIndexedFile {
             this.filehandle = filehandle;
         }
         else if (path) {
-            this.filehandle = new generic_filehandle_1.LocalFile(path);
+            this.filehandle = new generic_filehandle2_1.LocalFile(path);
         }
         else if (url) {
-            this.filehandle = new generic_filehandle_1.RemoteFile(url);
+            this.filehandle = new generic_filehandle2_1.RemoteFile(url);
         }
         else {
             throw new TypeError('must provide either filehandle or path');
@@ -70,35 +68,35 @@ class TabixIndexedFile {
         }
         else if (tbiPath) {
             this.index = new tbi_1.default({
-                filehandle: new generic_filehandle_1.LocalFile(tbiPath),
+                filehandle: new generic_filehandle2_1.LocalFile(tbiPath),
                 renameRefSeqs,
             });
         }
         else if (csiPath) {
             this.index = new csi_1.default({
-                filehandle: new generic_filehandle_1.LocalFile(csiPath),
+                filehandle: new generic_filehandle2_1.LocalFile(csiPath),
                 renameRefSeqs,
             });
         }
         else if (path) {
             this.index = new tbi_1.default({
-                filehandle: new generic_filehandle_1.LocalFile(`${path}.tbi`),
+                filehandle: new generic_filehandle2_1.LocalFile(`${path}.tbi`),
                 renameRefSeqs,
             });
         }
         else if (csiUrl) {
             this.index = new csi_1.default({
-                filehandle: new generic_filehandle_1.RemoteFile(csiUrl),
+                filehandle: new generic_filehandle2_1.RemoteFile(csiUrl),
             });
         }
         else if (tbiUrl) {
             this.index = new tbi_1.default({
-                filehandle: new generic_filehandle_1.RemoteFile(tbiUrl),
+                filehandle: new generic_filehandle2_1.RemoteFile(tbiUrl),
             });
         }
         else if (url) {
             this.index = new tbi_1.default({
-                filehandle: new generic_filehandle_1.RemoteFile(`${url}.tbi`),
+                filehandle: new generic_filehandle2_1.RemoteFile(`${url}.tbi`),
             });
         }
         else {
@@ -124,7 +122,6 @@ class TabixIndexedFile {
      * rejected on error
      */
     async getLines(refName, s, e, opts) {
-        var _a, _b;
         let signal;
         let options = {};
         let callback;
@@ -138,8 +135,8 @@ class TabixIndexedFile {
         }
         const metadata = await this.index.getMetadata(options);
         (0, util_1.checkAbortSignal)(signal);
-        const start = s !== null && s !== void 0 ? s : 0;
-        const end = e !== null && e !== void 0 ? e : metadata.maxRefLength;
+        const start = s ?? 0;
+        const end = e ?? metadata.maxRefLength;
         if (!(start <= end)) {
             throw new TypeError('invalid start and end coordinates. start must be less than or equal to end');
         }
@@ -148,17 +145,18 @@ class TabixIndexedFile {
         }
         const chunks = await this.index.blocksForRange(refName, start, end, options);
         (0, util_1.checkAbortSignal)(signal);
+        const decoder = new TextDecoder('utf8');
         // now go through each chunk and parse and filter the lines out of it
         for (const c of chunks) {
             const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
             (0, util_1.checkAbortSignal)(signal);
             let blockStart = 0;
             let pos = 0;
-            const str = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(buffer)) !== null && _a !== void 0 ? _a : buffer.toString();
             // 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
-            const strIsASCII = buffer.length < 500000000 && isASCII(str);
+            const str = decoder.decode(buffer);
+            const strIsASCII = isASCII(str);
             while (blockStart < str.length) {
                 let line;
                 let n;
@@ -170,12 +168,12 @@ class TabixIndexedFile {
                     line = str.slice(blockStart, n);
                 }
                 else {
-                    n = buffer.indexOf('\n', blockStart);
+                    n = buffer.indexOf('\n'.charCodeAt(0), blockStart);
                     if (n === -1) {
                         break;
                     }
                     const b = buffer.slice(blockStart, n);
-                    line = (_b = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _b !== void 0 ? _b : b.toString();
+                    line = decoder.decode(b);
                 }
                 // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 if (dpositions) {
@@ -222,10 +220,10 @@ class TabixIndexedFile {
     async getHeaderBuffer(opts = {}) {
         const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
         (0, util_1.checkAbortSignal)(opts.signal);
-        const maxFetch = ((firstDataLine === null || firstDataLine === void 0 ? void 0 : firstDataLine.blockPosition) || 0) + maxBlockSize;
-        // TODO: what if we don't have a firstDataLine, and the header
-        // actually takes up more than one block? this case is not covered here
-        const buf = await this._readRegion(0, maxFetch, opts);
+        const maxFetch = (firstDataLine?.blockPosition || 0) + maxBlockSize;
+        // TODO: what if we don't have a firstDataLine, and the header actually
+        // takes up more than one block? this case is not covered here
+        const buf = await this.filehandle.read(maxFetch, 0, opts);
         const bytes = await (0, bgzf_filehandle_1.unzip)(buf);
         // trim off lines after the last non-meta line
         if (metaChar) {
@@ -252,8 +250,9 @@ class TabixIndexedFile {
      * @returns {Promise} for a string
      */
     async getHeader(opts = {}) {
+        const decoder = new TextDecoder('utf8');
         const bytes = await this.getHeaderBuffer(opts);
-        return bytes.toString('utf8');
+        return decoder.decode(bytes);
     }
     /**
      * get an array of reference sequence names, in the order in which they occur
@@ -403,20 +402,13 @@ class TabixIndexedFile {
     async lineCount(refName, opts = {}) {
         return this.index.lineCount(refName, opts);
     }
-    async _readRegion(pos, size, opts = {}) {
-        const b = buffer_1.Buffer.alloc(size);
-        const { bytesRead, buffer } = await this.filehandle.read(b, 0, size, pos, opts);
-        return buffer.subarray(0, bytesRead);
-    }
     /**
      * read and uncompress the data in a chunk (composed of one or more
      * contiguous bgzip blocks) of the file
      */
     async readChunk(c, opts = {}) {
-        // fetch the uncompressed data, uncompress carefully a block at a time, and
-        // stop when done
-        const data = await this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
-        return (0, bgzf_filehandle_1.unzipChunkSlice)(data, c);
+        const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
+        return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c);
     }
 }
 exports.default = TabixIndexedFile;

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package/dist/tbi.d.ts

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile, { Options } from './indexFile';
@@ -28,10 +27,10 @@ export default class TabixIndex extends IndexFile {
         refNameToId: Record<string, number>;
         maxBlockSize: number;
     }>;
-    parsePseudoBin(bytes: Buffer, offset: number): {
+    parsePseudoBin(bytes: Uint8Array, offset: number): {
         lineCount: number;
     };
-    _parseNameBytes(namesBytes: Buffer): {
+    _parseNameBytes(namesBytes: Uint8Array): {
         refNameToId: Record<string, number>;
         refIdToName: string[];
     };

package/dist/tbi.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -61,25 +71,21 @@ class TabixIndex extends indexFile_1.default {
         if (!idx) {
             return -1;
         }
-        const { stats } = indexData.indices[refId];
-        if (stats) {
-            return stats.lineCount;
-        }
-        return -1;
+        return indexData.indices[refId].stats?.lineCount ?? -1;
     }
     // fetch and parse the index
     async _parse(opts = {}) {
         const buf = await this.filehandle.readFile(opts);
         const bytes = await (0, bgzf_filehandle_1.unzip)(buf);
         (0, util_1.checkAbortSignal)(opts.signal);
-        // check TBI magic numbers
-        if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
+        const dataView = new DataView(bytes.buffer);
+        const magic = dataView.getUint32(0, true);
+        if (magic !== TBI_MAGIC /* "TBI\1" */) {
             throw new Error('Not a TBI file');
-            // TODO: do we need to support big-endian TBI files?
         }
         // number of reference sequences in the index
-        const refCount = bytes.readInt32LE(4);
-        const formatFlags = bytes.readInt32LE(8);
+        const refCount = dataView.getUint32(4, true);
+        const formatFlags = dataView.getUint32(8, true);
         const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
         const formatOpts = {
             0: 'generic',
@@ -91,36 +97,36 @@ class TabixIndex extends indexFile_1.default {
             throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
         }
         const columnNumbers = {
-            ref: bytes.readInt32LE(12),
-            start: bytes.readInt32LE(16),
-            end: bytes.readInt32LE(20),
+            ref: dataView.getInt32(12, true),
+            start: dataView.getInt32(16, true),
+            end: dataView.getInt32(20, true),
         };
-        const metaValue = bytes.readInt32LE(24);
+        const metaValue = dataView.getInt32(24, true);
         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 skipLines = bytes.readInt32LE(28);
+        const skipLines = dataView.getInt32(28, true);
         // read sequence dictionary
-        const nameSectionLength = bytes.readInt32LE(32);
+        const nameSectionLength = dataView.getInt32(32, true);
         const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
         // read the indexes for each reference sequence
         let currOffset = 36 + nameSectionLength;
         let firstDataLine;
         const indices = new Array(refCount).fill(0).map(() => {
             // the binning index
-            const binCount = bytes.readInt32LE(currOffset);
+            const binCount = dataView.getInt32(currOffset, true);
             currOffset += 4;
             const binIndex = {};
             let stats;
             for (let j = 0; j < binCount; j += 1) {
-                const bin = bytes.readUInt32LE(currOffset);
+                const bin = dataView.getUint32(currOffset, true);
                 currOffset += 4;
                 if (bin > maxBinNumber + 1) {
                     throw new Error('tabix index contains too many bins, please use a CSI index');
                 }
                 else if (bin === maxBinNumber + 1) {
-                    const chunkCount = bytes.readInt32LE(currOffset);
+                    const chunkCount = dataView.getInt32(currOffset, true);
                     currOffset += 4;
                     if (chunkCount === 2) {
                         stats = this.parsePseudoBin(bytes, currOffset);
@@ -128,7 +134,7 @@ class TabixIndex extends indexFile_1.default {
                     currOffset += 16 * chunkCount;
                 }
                 else {
-                    const chunkCount = bytes.readInt32LE(currOffset);
+                    const chunkCount = dataView.getInt32(currOffset, true);
                     currOffset += 4;
                     const chunks = new Array(chunkCount);
                     for (let k = 0; k < chunkCount; k += 1) {
@@ -142,7 +148,7 @@ class TabixIndex extends indexFile_1.default {
                 }
             }
             // the linear index
-            const linearCount = bytes.readInt32LE(currOffset);
+            const linearCount = dataView.getInt32(currOffset, true);
             currOffset += 4;
             const linearIndex = new Array(linearCount);
             for (let k = 0; k < linearCount; k += 1) {
@@ -150,7 +156,11 @@ class TabixIndex extends indexFile_1.default {
                 currOffset += 8;
                 firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
             }
-            return { binIndex, linearIndex, stats };
+            return {
+                binIndex,
+                linearIndex,
+                stats,
+            };
         });
         return {
             indices,
@@ -168,7 +178,7 @@ class TabixIndex extends indexFile_1.default {
         };
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
+        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.subarray(offset + 16, offset + 24), true));
         return { lineCount };
     }
     _parseNameBytes(namesBytes) {
@@ -176,11 +186,11 @@ class TabixIndex extends indexFile_1.default {
         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) {
-                    let refName = namesBytes.toString('utf8', currNameStart, i);
-                    refName = this.renameRefSeq(refName);
+                    const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
                     refIdToName[currRefId] = refName;
                     refNameToId[refName] = currRefId;
                 }
@@ -188,7 +198,10 @@ class TabixIndex extends indexFile_1.default {
                 currRefId += 1;
             }
         }
-        return { refNameToId, refIdToName };
+        return {
+            refNameToId,
+            refIdToName,
+        };
     }
     async blocksForRange(refName, min, max, opts = {}) {
         if (min < 0) {

package/dist/tbi.js.map

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

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 export default class VirtualOffset {
     blockPosition: number;
     dataPosition: number;
@@ -6,4 +5,4 @@ export default class VirtualOffset {
     toString(): string;
     compareTo(b: VirtualOffset): number;
 }
-export declare function fromBytes(bytes: Buffer, offset?: number, bigendian?: boolean): VirtualOffset;
+export declare function fromBytes(bytes: Uint8Array, offset?: number): VirtualOffset;

package/dist/virtualOffset.js

@@ -14,10 +14,7 @@ class VirtualOffset {
     }
 }
 exports.default = VirtualOffset;
-function fromBytes(bytes, offset = 0, bigendian = false) {
-    if (bigendian) {
-        throw new Error('big-endian virtual file offsets not implemented');
-    }
+function fromBytes(bytes, offset = 0) {
     return new VirtualOffset(bytes[offset + 7] * 0x10000000000 +
         bytes[offset + 6] * 0x100000000 +
         bytes[offset + 5] * 0x1000000 +

package/dist/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;AAmBA,8BAcC;AAhCD,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;CACF;AAjBD,gCAiBC;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,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;AAkBA,8BAUC;AA5BD,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;CACF;AAjBD,gCAiBC;AACD,SAAgB,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC;IACrD,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}

package/esm/csi.d.ts

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile, { Options } from './indexFile';
@@ -9,7 +8,7 @@ export default class CSI extends IndexFile {
     constructor(args: any);
     lineCount(refName: string, opts?: Options): Promise<number>;
     indexCov(): void;
-    parseAuxData(bytes: Buffer, offset: number): {
+    parseAuxData(bytes: Uint8Array, offset: number): {
         refIdToName: string[];
         refNameToId: Record<string, number>;
         skipLines: number;
@@ -22,7 +21,7 @@ export default class CSI extends IndexFile {
         format: string;
         coordinateType: string;
     };
-    _parseNameBytes(namesBytes: Buffer): {
+    _parseNameBytes(namesBytes: Uint8Array): {
         refNameToId: Record<string, number>;
         refIdToName: string[];
     };
@@ -78,7 +77,7 @@ export default class CSI extends IndexFile {
         coordinateType: string;
         format: string;
     }>;
-    parsePseudoBin(bytes: Buffer, offset: number): {
+    parsePseudoBin(bytes: Uint8Array, offset: number): {
         lineCount: number;
     };
     blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;