@gmod/tabix 1.5.15 → 1.6.0

package/dist/tabixIndexedFile.d.ts

@@ -11,7 +11,6 @@ interface GetLinesOpts {
 export default class TabixIndexedFile {
     private filehandle;
     private index;
-    private yieldTime;
     private renameRefSeq;
     private chunkCache;
     /**
@@ -29,15 +28,18 @@ export default class TabixIndexedFile {
      *
      * @param {filehandle} [args.csiFilehandle]
      *
-     * @param {number} [args.yieldTime] yield to main thread after N milliseconds
-     * if reading features is taking a long time to avoid hanging main thread
+     * @param {url} [args.url]
+     *
+     * @param {csiUrl} [args.csiUrl]
+     *
+     * @param {tbiUrl} [args.tbiUrl]
      *
      * @param {function} [args.renameRefSeqs] optional function with sig `string
      * => string` to transform reference sequence names for the purpose of
      * indexing and querying. note that the data that is returned is not altered,
      * just the names of the reference sequences that are used for querying.
      */
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, yieldTime, renameRefSeqs, chunkCacheSize, }: {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs, chunkCacheSize, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         url?: string;
@@ -47,7 +49,6 @@ export default class TabixIndexedFile {
         csiPath?: string;
         csiUrl?: string;
         csiFilehandle?: GenericFilehandle;
-        yieldTime?: number;
         renameRefSeqs?: (n: string) => string;
         chunkCacheSize?: number;
     });
@@ -82,7 +83,7 @@ export default class TabixIndexedFile {
      * get a buffer containing the "header" region of the file, which are the
      * bytes up to the first non-meta line
      */
-    getHeaderBuffer(opts?: Options): Promise<Buffer>;
+    getHeaderBuffer(opts?: Options): Promise<Buffer<Uint8Array<ArrayBuffer>>>;
     /**
      * get a string containing the "header" region of the file, is the portion up
      * to the first non-meta line
@@ -127,13 +128,13 @@ export default class TabixIndexedFile {
      * @returns number of data lines present on that reference sequence
      */
     lineCount(refName: string, opts?: Options): Promise<number>;
-    _readRegion(pos: number, size: number, opts?: Options): Promise<Buffer>;
+    _readRegion(pos: number, size: number, opts?: Options): Promise<Buffer<ArrayBufferLike>>;
     /**
      * read and uncompress the data in a chunk (composed of one or more
      * contiguous bgzip blocks) of the file
      */
     readChunk(c: Chunk, opts?: Options): Promise<{
-        buffer: Buffer;
+        buffer: Buffer<Uint8Array<ArrayBuffer>>;
         cpositions: number[];
         dpositions: number[];
     }>;

package/dist/tabixIndexedFile.js

@@ -1,13 +1,4 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -20,10 +11,11 @@ const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const util_1 = require("./util");
 const tbi_1 = __importDefault(require("./tbi"));
 const csi_1 = __importDefault(require("./csi"));
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
-function timeout(time) {
-    return new Promise(resolve => setTimeout(resolve, time));
+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
@@ -40,15 +32,18 @@ class TabixIndexedFile {
      *
      * @param {filehandle} [args.csiFilehandle]
      *
-     * @param {number} [args.yieldTime] yield to main thread after N milliseconds
-     * if reading features is taking a long time to avoid hanging main thread
+     * @param {url} [args.url]
+     *
+     * @param {csiUrl} [args.csiUrl]
+     *
+     * @param {tbiUrl} [args.tbiUrl]
      *
      * @param {function} [args.renameRefSeqs] optional function with sig `string
      * => string` to transform reference sequence names for the purpose of
      * indexing and querying. note that the data that is returned is not altered,
      * just the names of the reference sequences that are used for querying.
      */
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, yieldTime = 500, renameRefSeqs = n => n, chunkCacheSize = 5 * Math.pow(2, 20), }) {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -110,7 +105,6 @@ class TabixIndexedFile {
             throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
         }
         this.renameRefSeq = renameRefSeqs;
-        this.yieldTime = yieldTime;
         this.chunkCache = new abortable_promise_cache_1.default({
             cache: new quick_lru_1.default({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
             fill: (args, signal) => this.readChunk(args, { signal }),
@@ -129,131 +123,128 @@ class TabixIndexedFile {
      * @returns promise that is resolved when the whole read is finished,
      * rejected on error
      */
-    getLines(refName, s, e, opts) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            let signal;
-            let options = {};
-            let callback;
-            if (typeof opts === 'function') {
-                callback = opts;
-            }
-            else {
-                options = opts;
-                callback = opts.lineCallback;
-                signal = opts.signal;
-            }
-            const metadata = yield 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;
-            if (!(start <= end)) {
-                throw new TypeError('invalid start and end coordinates. start must be less than or equal to end');
-            }
-            if (start === end) {
-                return;
-            }
-            const chunks = yield this.index.blocksForRange(refName, start, end, options);
+    async getLines(refName, s, e, opts) {
+        var _a, _b;
+        let signal;
+        let options = {};
+        let callback;
+        if (typeof opts === 'function') {
+            callback = opts;
+        }
+        else {
+            options = opts;
+            callback = opts.lineCallback;
+            signal = opts.signal;
+        }
+        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;
+        if (!(start <= end)) {
+            throw new TypeError('invalid start and end coordinates. start must be less than or equal to end');
+        }
+        if (start === end) {
+            return;
+        }
+        const chunks = await this.index.blocksForRange(refName, start, end, options);
+        (0, util_1.checkAbortSignal)(signal);
+        // 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);
-            // now go through each chunk and parse and filter the lines out of it
-            let last = Date.now();
-            for (const c of chunks) {
-                let previousStartCoordinate;
-                const { buffer, cpositions, dpositions } = yield this.chunkCache.get(c.toString(), c, signal);
-                (0, util_1.checkAbortSignal)(signal);
-                let blockStart = 0;
-                let pos = 0;
-                while (blockStart < buffer.length) {
-                    const n = buffer.indexOf('\n', blockStart);
+            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);
+            while (blockStart < str.length) {
+                let line;
+                let n;
+                if (strIsASCII) {
+                    n = str.indexOf('\n', blockStart);
                     if (n === -1) {
                         break;
                     }
-                    const b = buffer.slice(blockStart, n);
-                    const line = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
-                    // 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);
-                    // do a small check just to make sure that the lines are really sorted
-                    // by start coordinate
-                    if (previousStartCoordinate !== undefined &&
-                        startCoordinate !== undefined &&
-                        previousStartCoordinate > startCoordinate) {
-                        throw new Error(`Lines not sorted by start coordinate (${previousStartCoordinate} > ${startCoordinate}), this file is not usable with Tabix.`);
-                    }
-                    previousStartCoordinate = startCoordinate;
-                    if (overlaps) {
-                        callback(line.trim(), 
-                        // 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;
-                    }
-                    // yield if we have emitted beyond the yield limit
-                    if (this.yieldTime && last - Date.now() > this.yieldTime) {
-                        last = Date.now();
-                        (0, util_1.checkAbortSignal)(signal);
-                        yield timeout(1);
+                    line = str.slice(blockStart, n);
+                }
+                else {
+                    n = buffer.indexOf('\n', blockStart);
+                    if (n === -1) {
+                        break;
                     }
-                    blockStart = n + 1;
+                    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();
+                }
+                // 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;
                 }
+                blockStart = n + 1;
             }
-        });
+        }
     }
-    getMetadata() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            return this.index.getMetadata(opts);
-        });
+    async getMetadata(opts = {}) {
+        return this.index.getMetadata(opts);
     }
     /**
      * get a buffer containing the "header" region of the file, which are the
      * bytes up to the first non-meta line
      */
-    getHeaderBuffer() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            const { firstDataLine, metaChar, maxBlockSize } = yield this.getMetadata(opts);
-            (0, util_1.checkAbortSignal)(opts.signal);
-            // eslint-disable-next-line @typescript-eslint/restrict-plus-operands
-            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 = yield this._readRegion(0, maxFetch, opts);
-            const bytes = yield (0, bgzf_filehandle_1.unzip)(buf);
-            // trim off lines after the last non-meta line
-            if (metaChar) {
-                // trim backward from the end
-                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) {
-                        break;
-                    }
-                    if (bytes[i] === newlineByte) {
-                        lastNewline = i;
-                    }
+    async getHeaderBuffer(opts = {}) {
+        const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
+        (0, util_1.checkAbortSignal)(opts.signal);
+        // eslint-disable-next-line @typescript-eslint/restrict-plus-operands
+        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 bytes = await (0, bgzf_filehandle_1.unzip)(buf);
+        // trim off lines after the last non-meta line
+        if (metaChar) {
+            // trim backward from the end
+            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) {
+                    break;
+                }
+                if (bytes[i] === newlineByte) {
+                    lastNewline = i;
                 }
-                return bytes.slice(0, lastNewline + 1);
             }
-            return bytes;
-        });
+            return bytes.subarray(0, lastNewline + 1);
+        }
+        return bytes;
     }
     /**
      * get a string containing the "header" region of the file, is the portion up
@@ -261,21 +252,17 @@ class TabixIndexedFile {
      *
      * @returns {Promise} for a string
      */
-    getHeader() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            const bytes = yield this.getHeaderBuffer(opts);
-            return bytes.toString('utf8');
-        });
+    async getHeader(opts = {}) {
+        const bytes = await this.getHeaderBuffer(opts);
+        return bytes.toString('utf8');
     }
     /**
      * get an array of reference sequence names, in the order in which they occur
      * in the file. reference sequence renaming is not applied to these names.
      */
-    getReferenceSequenceNames() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            const metadata = yield this.getMetadata(opts);
-            return metadata.refIdToName;
-        });
+    async getReferenceSequenceNames(opts = {}) {
+        const metadata = await this.getMetadata(opts);
+        return metadata.refIdToName;
     }
     /**
      * @param {object} metadata metadata object from the parsed index, containing
@@ -320,12 +307,15 @@ class TabixIndexedFile {
         let currentColumnStart = 0;
         let refSeq = '';
         let startCoordinate = -Infinity;
-        for (let i = 0; i < line.length + 1; i += 1) {
-            if (line[i] === '\t' || i === line.length) {
+        const l = line.length;
+        for (let i = 0; i < l + 1; i++) {
+            if (line[i] === '\t' || i === l) {
                 if (currentColumnNumber === ref) {
                     if (this.renameRefSeq(line.slice(currentColumnStart, i)) !==
                         regionRefName) {
-                        return { overlaps: false };
+                        return {
+                            overlaps: false,
+                        };
                     }
                 }
                 else if (currentColumnNumber === start) {
@@ -335,12 +325,18 @@ class TabixIndexedFile {
                         startCoordinate -= 1;
                     }
                     if (startCoordinate >= regionEnd) {
-                        return { startCoordinate, overlaps: false };
+                        return {
+                            startCoordinate,
+                            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 };
+                            return {
+                                startCoordinate,
+                                overlaps: false,
+                            };
                         }
                     }
                 }
@@ -351,9 +347,11 @@ class TabixIndexedFile {
                     // this will never match if there is no end column
                     const endCoordinate = format === 'VCF'
                         ? this._getVcfEnd(startCoordinate, refSeq, line.slice(currentColumnStart, i))
-                        : parseInt(line.slice(currentColumnStart, i), 10);
+                        : Number.parseInt(line.slice(currentColumnStart, i), 10);
                     if (endCoordinate <= regionStart) {
-                        return { overlaps: false };
+                        return {
+                            overlaps: false,
+                        };
                     }
                 }
                 currentColumnStart = i + 1;
@@ -363,7 +361,10 @@ class TabixIndexedFile {
                 }
             }
         }
-        return { startCoordinate, overlaps: true };
+        return {
+            startCoordinate,
+            overlaps: true,
+        };
     }
     _getVcfEnd(startCoordinate, refSeq, info) {
         let endCoordinate = startCoordinate + refSeq.length;
@@ -400,29 +401,23 @@ class TabixIndexedFile {
      *
      * @returns number of data lines present on that reference sequence
      */
-    lineCount(refName_1) {
-        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
-            return this.index.lineCount(refName, opts);
-        });
+    async lineCount(refName, opts = {}) {
+        return this.index.lineCount(refName, opts);
     }
-    _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);
-        });
+    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
      */
-    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);
-            return (0, bgzf_filehandle_1.unzipChunkSlice)(data, c);
-        });
+    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);
     }
 }
 exports.default = TabixIndexedFile;

package/dist/tabixIndexedFile.js.map

@@ -1 +1 @@
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