@gmod/tabix 3.2.0 → 3.2.2

package/dist/tabixIndexedFile.d.ts

@@ -1,8 +1,8 @@
-import LRU from 'quick-lru';
+import LRU from '@jbrowse/quick-lru';
 import Chunk from './chunk.ts';
-import { IndexData, Options } from './indexFile.ts';
+import { Options } from './indexFile.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
-type GetLinesCallback = (line: string, fileOffset: number) => void;
+type GetLinesCallback = (line: string, fileOffset: number, start: number, end: number) => void;
 interface GetLinesOpts {
     [key: string]: unknown;
     signal?: AbortSignal;
@@ -12,6 +12,7 @@ export default class TabixIndexedFile {
     private filehandle;
     private index;
     private renameRefSeq;
+    private hasCustomRenameRefSeq;
     private chunkCache;
     cache: LRU<string, {
         bytesRead: number;
@@ -44,7 +45,7 @@ export default class TabixIndexedFile {
      * 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, renameRefSeqs, chunkCacheSize, }: {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs: renameRefSeqsPre, chunkCacheSize, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         url?: string;
@@ -89,12 +90,10 @@ 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<Uint8Array<ArrayBufferLike>>;
+    getHeaderBuffer(opts?: Options): Promise<any>;
     /**
      * get a string containing the "header" region of the file, is the portion up
      * to the first non-meta line
-     *
-     * @returns {Promise} for a string
      */
     getHeader(opts?: Options): Promise<string>;
     /**
@@ -103,27 +102,36 @@ export default class TabixIndexedFile {
      */
     getReferenceSequenceNames(opts?: Options): Promise<string[]>;
     /**
-     * @param {object} metadata metadata object from the parsed index, containing
-     * columnNumbers, metaChar, and format
-     *
      * @param {string} regionRefName
      *
      * @param {number} regionStart region start coordinate (0-based-half-open)
      *
      * @param {number} regionEnd region end coordinate (0-based-half-open)
      *
-     * @param {array[string]} line
+     * @param {string} line
+     *
+     * @param {number} refColumn column number for ref
+     *
+     * @param {number} startColumn column number for start
+     *
+     * @param {number} endColumn column number for end
+     *
+     * @param {number} maxColumn pre-calculated max column
+     *
+     * @param {number} metaCharCode pre-calculated metaChar code
+     *
+     * @param {number} coordinateOffset 0 or -1 for coordinate adjustment
+     *
+     * @param {boolean} isVCF whether this is VCF format
+     *
+     * @param {boolean} isIdentityRename whether renameRefSeq is the identity function
      *
-     * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
-     * true if line is a data line that overlaps the given region
+     * @returns {{ start: number, end: number } | null | undefined} coordinates if overlapping, null if should stop processing, undefined otherwise
      */
-    checkLine(metadata: IndexData, regionRefName: string, regionStart: number, regionEnd: number, line: string): {
-        overlaps: boolean;
-        startCoordinate?: undefined;
-    } | {
-        startCoordinate: number;
-        overlaps: boolean;
-    };
+    checkLine(regionRefName: string, regionStart: number, regionEnd: number, line: string, refColumn: number, startColumn: number, endColumn: number, maxColumn: number, metaCharCode: number | undefined, coordinateOffset: number, isVCF: boolean, isIdentityRename: boolean): {
+        start: number;
+        end: number;
+    } | null | undefined;
     _getVcfEnd(startCoordinate: number, refSeq: string, info: any): number;
     /**
      * return the approximate number of data lines in the given reference

package/dist/tabixIndexedFile.js

@@ -5,11 +5,10 @@ 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 bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
 const generic_filehandle2_1 = require("generic-filehandle2");
-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");
 class TabixIndexedFile {
     /**
      * @param {object} args
@@ -37,10 +36,11 @@ class TabixIndexedFile {
      * 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, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs: renameRefSeqsPre, chunkCacheSize = 5 * 2 ** 20, }) {
         this.cache = new quick_lru_1.default({
             maxSize: 1000,
         });
+        const renameRefSeqs = renameRefSeqsPre ?? (arg => arg);
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -102,6 +102,7 @@ class TabixIndexedFile {
             throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
         }
         this.renameRefSeq = renameRefSeqs;
+        this.hasCustomRenameRefSeq = renameRefSeqsPre !== undefined;
         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 }),
@@ -139,7 +140,6 @@ class TabixIndexedFile {
             signal = opts.signal;
         }
         const metadata = await this.index.getMetadata(options);
-        (0, util_ts_1.checkAbortSignal)(signal);
         const start = s ?? 0;
         const end = e ?? metadata.maxRefLength;
         if (!(start <= end)) {
@@ -149,12 +149,20 @@ class TabixIndexedFile {
             return;
         }
         const chunks = await this.index.blocksForRange(refName, start, end, options);
-        (0, util_ts_1.checkAbortSignal)(signal);
         const decoder = new TextDecoder('utf8');
+        const isVCF = metadata.format === 'VCF';
+        const columnNumbersEffective = {
+            ref: metadata.columnNumbers.ref || 0,
+            start: metadata.columnNumbers.start || 0,
+            end: isVCF ? 8 : metadata.columnNumbers.end || 0,
+        };
+        const maxColumn = Math.max(columnNumbersEffective.ref, columnNumbersEffective.start, columnNumbersEffective.end);
+        const metaCharCode = metadata.metaChar?.charCodeAt(0);
+        const coordinateOffset = metadata.coordinateType === '1-based-closed' ? -1 : 0;
+        const isIdentityRename = !this.hasCustomRenameRefSeq;
         // 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_ts_1.checkAbortSignal)(signal);
             let blockStart = 0;
             let pos = 0;
             // fast path, Buffer is just ASCII chars and not gigantor, can be
@@ -182,16 +190,13 @@ class TabixIndexedFile {
                         }
                     }
                     // 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
+                    const result = this.checkLine(refName, start, end, line, columnNumbersEffective.ref, columnNumbersEffective.start, columnNumbersEffective.end, maxColumn, metaCharCode, coordinateOffset, isVCF, isIdentityRename);
+                    if (result === null) {
                         return;
                     }
+                    else if (result !== undefined) {
+                        callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition), result.start, result.end);
+                    }
                     blockStart = n + 1;
                 }
             }
@@ -211,16 +216,13 @@ class TabixIndexedFile {
                         }
                     }
                     // 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
+                    const result = this.checkLine(refName, start, end, line, columnNumbersEffective.ref, columnNumbersEffective.start, columnNumbersEffective.end, maxColumn, metaCharCode, coordinateOffset, isVCF, isIdentityRename);
+                    if (result === null) {
                         return;
                     }
+                    else if (result !== undefined) {
+                        callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition), result.start, result.end);
+                    }
                     blockStart = n + 1;
                 }
             }
@@ -235,7 +237,6 @@ class TabixIndexedFile {
      */
     async getHeaderBuffer(opts = {}) {
         const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
-        (0, util_ts_1.checkAbortSignal)(opts.signal);
         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
@@ -263,8 +264,6 @@ class TabixIndexedFile {
     /**
      * get a string containing the "header" region of the file, is the portion up
      * to the first non-meta line
-     *
-     * @returns {Promise} for a string
      */
     async getHeader(opts = {}) {
         const decoder = new TextDecoder('utf8');
@@ -280,123 +279,122 @@ class TabixIndexedFile {
         return metadata.refIdToName;
     }
     /**
-     * @param {object} metadata metadata object from the parsed index, containing
-     * columnNumbers, metaChar, and format
-     *
      * @param {string} regionRefName
      *
      * @param {number} regionStart region start coordinate (0-based-half-open)
      *
      * @param {number} regionEnd region end coordinate (0-based-half-open)
      *
-     * @param {array[string]} line
+     * @param {string} line
+     *
+     * @param {number} refColumn column number for ref
+     *
+     * @param {number} startColumn column number for start
+     *
+     * @param {number} endColumn column number for end
+     *
+     * @param {number} maxColumn pre-calculated max column
+     *
+     * @param {number} metaCharCode pre-calculated metaChar code
      *
-     * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
-     * true if line is a data line that overlaps the given region
+     * @param {number} coordinateOffset 0 or -1 for coordinate adjustment
+     *
+     * @param {boolean} isVCF whether this is VCF format
+     *
+     * @param {boolean} isIdentityRename whether renameRefSeq is the identity function
+     *
+     * @returns {{ start: number, end: number } | null | undefined} coordinates if overlapping, null if should stop processing, undefined otherwise
      */
-    checkLine(metadata, regionRefName, regionStart, regionEnd, line) {
-        const { columnNumbers, metaChar, coordinateType, format } = metadata;
-        // skip meta lines
-        if (metaChar && line.startsWith(metaChar)) {
-            return { overlaps: false };
+    checkLine(regionRefName, regionStart, regionEnd, line, refColumn, startColumn, endColumn, maxColumn, metaCharCode, coordinateOffset, isVCF, isIdentityRename) {
+        if (metaCharCode !== undefined && line.charCodeAt(0) === metaCharCode) {
+            return;
+        }
+        // Length-based fast path: split for short lines, indexOf for long lines
+        // Split is faster for short lines, but slow for long lines with big attribute columns
+        if (line.length < 500) {
+            const fields = line.split('\t');
+            const ref = fields[refColumn - 1];
+            const refMatch = isIdentityRename
+                ? ref === regionRefName
+                : this.renameRefSeq(ref) === regionRefName;
+            if (!refMatch) {
+                return;
+            }
+            const startCoordinate = +fields[startColumn - 1] + coordinateOffset;
+            if (startCoordinate >= regionEnd) {
+                return null;
+            }
+            let endCoordinate;
+            if (endColumn === 0 || endColumn === startColumn) {
+                endCoordinate = startCoordinate + 1;
+            }
+            else if (isVCF) {
+                endCoordinate = this._getVcfEnd(startCoordinate, fields[3], fields[endColumn - 1]);
+            }
+            else {
+                endCoordinate = +fields[endColumn - 1];
+            }
+            if (endCoordinate <= regionStart) {
+                return;
+            }
+            return { start: startCoordinate, end: endCoordinate };
         }
-        // check ref/start/end using column metadata from index
-        let { ref, start, end } = columnNumbers;
-        if (!ref) {
-            ref = 0;
+        // Long lines - use indexOf chain (avoids parsing long attribute column)
+        let prev = -1;
+        const tabs = [-1];
+        for (let i = 0; i < maxColumn; i++) {
+            const pos = line.indexOf('\t', prev + 1);
+            if (pos === -1) {
+                tabs.push(line.length);
+                break;
+            }
+            tabs.push(pos);
+            prev = pos;
         }
-        if (!start) {
-            start = 0;
+        const ref = line.slice(tabs[refColumn - 1] + 1, tabs[refColumn]);
+        const refMatch = isIdentityRename
+            ? ref === regionRefName
+            : this.renameRefSeq(ref) === regionRefName;
+        if (!refMatch) {
+            return;
         }
-        if (!end) {
-            end = 0;
+        const startCoordinate = +line.slice(tabs[startColumn - 1] + 1, tabs[startColumn]) +
+            coordinateOffset;
+        if (startCoordinate >= regionEnd) {
+            return null;
         }
-        if (format === 'VCF') {
-            end = 8;
+        let endCoordinate;
+        if (endColumn === 0 || endColumn === startColumn) {
+            endCoordinate = startCoordinate + 1;
         }
-        const maxColumn = Math.max(ref, start, end);
-        // this code is kind of complex, but it is fairly fast. basically, we want
-        // to avoid doing a split, because if the lines are really long that could
-        // lead to us allocating a bunch of extra memory, which is slow
-        let currentColumnNumber = 1; // cols are numbered starting at 1 in the index metadata
-        let currentColumnStart = 0;
-        let refSeq = '';
-        let startCoordinate = -Infinity;
-        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,
-                        };
-                    }
-                }
-                else if (currentColumnNumber === start) {
-                    startCoordinate = Number.parseInt(line.slice(currentColumnStart, i), 10);
-                    // we convert to 0-based-half-open
-                    if (coordinateType === '1-based-closed') {
-                        startCoordinate -= 1;
-                    }
-                    if (startCoordinate >= regionEnd) {
-                        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) {
-                    refSeq = line.slice(currentColumnStart, i);
-                }
-                else if (currentColumnNumber === end) {
-                    // this will never match if there is no end column
-                    const endCoordinate = format === 'VCF'
-                        ? this._getVcfEnd(startCoordinate, refSeq, line.slice(currentColumnStart, i))
-                        : Number.parseInt(line.slice(currentColumnStart, i), 10);
-                    if (endCoordinate <= regionStart) {
-                        return {
-                            overlaps: false,
-                        };
-                    }
-                }
-                if (currentColumnNumber === maxColumn) {
-                    break;
-                }
-                currentColumnStart = i + 1;
-                currentColumnNumber += 1;
-            }
+        else if (isVCF) {
+            endCoordinate = this._getVcfEnd(startCoordinate, line.slice(tabs[3] + 1, tabs[4]), line.slice(tabs[endColumn - 1] + 1, tabs[endColumn]));
         }
-        return {
-            startCoordinate,
-            overlaps: true,
-        };
+        else {
+            endCoordinate = +line.slice(tabs[endColumn - 1] + 1, tabs[endColumn]);
+        }
+        if (endCoordinate <= regionStart) {
+            return;
+        }
+        return { start: startCoordinate, end: endCoordinate };
     }
     _getVcfEnd(startCoordinate, refSeq, info) {
         let endCoordinate = startCoordinate + refSeq.length;
-        // ignore TRA features as they specify CHR2 and END as being on a different
-        // chromosome
-        //
-        // if CHR2 is on the same chromosome, still ignore it because there should
-        // be another pairwise feature at the end of this one
         const isTRA = info.includes('SVTYPE=TRA');
-        if (info[0] !== '.' && !isTRA) {
-            const endRegex = /(?:^|;)END=([^;]+)/;
-            const match = endRegex.exec(info);
-            if (match) {
-                endCoordinate = Number.parseInt(match[1], 10);
-            }
-        }
-        else if (isTRA) {
+        if (isTRA) {
             return startCoordinate + 1;
         }
+        if (info[0] !== '.') {
+            const endIdx = info.indexOf('END=');
+            if (endIdx !== -1 && (endIdx === 0 || info[endIdx - 1] === ';')) {
+                const start = endIdx + 4;
+                let end = info.indexOf(';', start);
+                if (end === -1) {
+                    end = info.length;
+                }
+                endCoordinate = Number.parseInt(info.slice(start, end), 10);
+            }
+        }
         return endCoordinate;
     }
     /**

package/dist/tabixIndexedFile.js.map

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

@@ -77,7 +77,6 @@ class TabixIndex extends indexFile_ts_1.default {
     async _parse(opts = {}) {
         const buf = await this.filehandle.readFile(opts);
         const bytes = await (0, bgzf_filehandle_1.unzip)(buf);
-        (0, util_ts_1.checkAbortSignal)(opts.signal);
         const dataView = new DataView(bytes.buffer);
         const magic = dataView.getUint32(0, true);
         if (magic !== TBI_MAGIC /* "TBI\1" */) {

package/dist/tbi.js.map

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

@@ -1,24 +1,4 @@
 import Chunk from './chunk.ts';
 import VirtualOffset from './virtualOffset.ts';
-/**
- * Properly check if the given AbortSignal is aborted. Per the standard, if the
- * signal reads as aborted, this function throws either a DOMException
- * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
- *
- * For convenience, passing `undefined` is a no-op
- *
- * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`
- * attribute
- *
- * @returns nothing
- */
-export declare function checkAbortSignal(signal?: AbortSignal): void;
-/**
- * Skips to the next tick, then runs `checkAbortSignal`.
- * Await this to inside an otherwise synchronous loop to
- * provide a place to break when an abort signal is received.
- * @param {AbortSignal} signal
- */
-export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
 export declare function canMergeBlocks(chunk1: Chunk, chunk2: Chunk): boolean;
 export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];

package/dist/util.js

@@ -1,48 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.checkAbortSignal = checkAbortSignal;
-exports.abortBreakPoint = abortBreakPoint;
 exports.canMergeBlocks = canMergeBlocks;
 exports.optimizeChunks = optimizeChunks;
-class AbortError extends Error {
-}
-/**
- * Properly check if the given AbortSignal is aborted. Per the standard, if the
- * signal reads as aborted, this function throws either a DOMException
- * AbortError, or a regular error with a `code` attribute set to `ERR_ABORTED`.
- *
- * For convenience, passing `undefined` is a no-op
- *
- * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted`
- * attribute
- *
- * @returns nothing
- */
-function checkAbortSignal(signal) {
-    if (!signal) {
-        return;
-    }
-    if (signal.aborted) {
-        if (typeof DOMException === 'undefined') {
-            const e = new AbortError('aborted');
-            e.code = 'ERR_ABORTED';
-            throw e;
-        }
-        else {
-            throw new DOMException('aborted', 'AbortError');
-        }
-    }
-}
-/**
- * Skips to the next tick, then runs `checkAbortSignal`.
- * Await this to inside an otherwise synchronous loop to
- * provide a place to break when an abort signal is received.
- * @param {AbortSignal} signal
- */
-async function abortBreakPoint(signal) {
-    await Promise.resolve();
-    checkAbortSignal(signal);
-}
 function canMergeBlocks(chunk1, chunk2) {
     return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
         chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);

package/dist/util.js.map

@@ -1 +1 @@
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