@gmod/tabix 1.5.6 → 1.5.7

package/esm/tabixIndexedFile.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="node" />
 import { GenericFilehandle } from 'generic-filehandle';
-import { Options } from './indexFile';
+import { Options, IndexData } from './indexFile';
 import Chunk from './chunk';
 type GetLinesCallback = (line: string, fileOffset: number) => void;
 interface GetLinesOpts {
@@ -12,6 +12,7 @@ export default class TabixIndexedFile {
     private filehandle;
     private index;
     private chunkSizeLimit;
+    private yieldTime;
     private renameRefSeq;
     private chunkCache;
     /**
@@ -22,39 +23,50 @@ export default class TabixIndexedFile {
      * @param {filehandle} [args.tbiFilehandle]
      * @param {string} [args.csiPath]
      * @param {filehandle} [args.csiFilehandle]
-     * @param {chunkSizeLimit} default 50MiB
+     * @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 {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.
-     * @param {number} [args.chunkCacheSize] maximum size in bytes of the chunk cache. default 5MB
-     * @param {number} [args.blockCacheSize] maximum size in bytes of the block cache. default 5MB
      */
-    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, chunkSizeLimit, renameRefSeqs, chunkCacheSize, }: {
+    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, yieldTime, chunkSizeLimit, renameRefSeqs, chunkCacheSize, }: {
         path?: string;
         filehandle?: GenericFilehandle;
         tbiPath?: string;
         tbiFilehandle?: GenericFilehandle;
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
+        yieldTime: number;
         chunkSizeLimit?: number;
         renameRefSeqs?: (n: string) => string;
         chunkCacheSize?: number;
     });
     /**
-     * @param {string} refName name of the reference sequence
-     * @param {number} start start of the region (in 0-based half-open coordinates)
-     * @param {number} end end of the region (in 0-based half-open coordinates)
-     * @param {function|object} lineCallback callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
-     * @returns {Promise} resolved when the whole read is finished, rejected on error
+     * @param refName name of the reference sequence
+     * @param start start of the region (in 0-based half-open coordinates)
+     * @param end end of the region (in 0-based half-open coordinates)
+     * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
+     * @returns promise that is resolved when the whole read is finished, rejected on error
      */
     getLines(refName: string, start: number, end: number, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
-    getMetadata(opts?: Options): Promise<any>;
+    getMetadata(opts?: Options): Promise<{
+        [key: string]: any;
+        refNameToId: {
+            [key: string]: number;
+        };
+        refIdToName: string[];
+        metaChar: string | null;
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        coordinateType: string;
+        format: string;
+    }>;
     /**
      * get a buffer containing the "header" region of
      * the file, which are the bytes up to the first
      * non-meta line
-     *
-     * @returns {Promise} for a buffer
      */
     getHeaderBuffer(opts?: Options): Promise<Buffer>;
     /**
@@ -66,13 +78,10 @@ export default class TabixIndexedFile {
     getHeader(opts?: Options): Promise<string>;
     /**
      * 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.
-     *
-     * @returns {Promise} for an array of string sequence names
+     * they occur in the file. reference sequence renaming is not applied
+     * to these names.
      */
-    getReferenceSequenceNames(opts?: Options): Promise<any>;
+    getReferenceSequenceNames(opts?: Options): Promise<string[]>;
     /**
      * @param {object} metadata metadata object from the parsed index,
      * containing columnNumbers, metaChar, and format
@@ -83,16 +92,7 @@ export default class TabixIndexedFile {
      * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
      * true if line is a data line that overlaps the given region
      */
-    checkLine({ columnNumbers, metaChar, coordinateType, format, }: {
-        columnNumbers: {
-            ref: number;
-            start: number;
-            end: number;
-        };
-        metaChar: string;
-        coordinateType: string;
-        format: string;
-    }, regionRefName: string, regionStart: number, regionEnd: number, line: string): {
+    checkLine(metadata: IndexData, regionRefName: string, regionStart: number, regionEnd: number, line: string): {
         overlaps: boolean;
         startCoordinate?: undefined;
     } | {
@@ -102,17 +102,19 @@ export default class TabixIndexedFile {
     _getVcfEnd(startCoordinate: number, refSeq: string, info: any): number;
     /**
      * return the approximate number of data lines in the given reference sequence
-     * @param {string} refSeq reference sequence name
-     * @returns {Promise} for number of data lines present on that reference sequence
+     * @param refSeq reference sequence name
+     * @returns number of data lines present on that reference sequence
      */
     lineCount(refName: string, opts?: Options): Promise<number>;
-    _readRegion(position: number, compressedSize: number, opts?: Options): Promise<Buffer>;
+    _readRegion(pos: number, size: number, opts?: Options): Promise<Buffer>;
     /**
      * read and uncompress the data in a chunk (composed of one or more
      * contiguous bgzip blocks) of the file
-     * @param {Chunk} chunk
-     * @returns {Promise} for a string chunk of the file
      */
-    readChunk(chunk: Chunk, opts?: Options): Promise<any>;
+    readChunk(c: Chunk, opts?: Options): Promise<{
+        buffer: Buffer;
+        cpositions: number[];
+        dpositions: number[];
+    }>;
 }
 export {};

package/esm/tabixIndexedFile.js

@@ -7,9 +7,7 @@ import TBI from './tbi';
 import CSI from './csi';
 const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined;
 function timeout(time) {
-    return new Promise(resolve => {
-        setTimeout(resolve, time);
-    });
+    return new Promise(resolve => setTimeout(resolve, time));
 }
 export default class TabixIndexedFile {
     /**
@@ -20,14 +18,12 @@ export default class TabixIndexedFile {
      * @param {filehandle} [args.tbiFilehandle]
      * @param {string} [args.csiPath]
      * @param {filehandle} [args.csiFilehandle]
-     * @param {chunkSizeLimit} default 50MiB
+     * @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 {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.
-     * @param {number} [args.chunkCacheSize] maximum size in bytes of the chunk cache. default 5MB
-     * @param {number} [args.blockCacheSize] maximum size in bytes of the block cache. default 5MB
      */
-    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, chunkSizeLimit = 50000000, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
+    constructor({ path, filehandle, tbiPath, tbiFilehandle, csiPath, csiFilehandle, yieldTime = 500, chunkSizeLimit = 50000000, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -72,19 +68,18 @@ export default class TabixIndexedFile {
         }
         this.chunkSizeLimit = chunkSizeLimit;
         this.renameRefSeq = renameRefSeqs;
+        this.yieldTime = yieldTime;
         this.chunkCache = new AbortablePromiseCache({
-            cache: new LRU({
-                maxSize: Math.floor(chunkCacheSize / (1 << 16)),
-            }),
-            fill: this.readChunk.bind(this),
+            cache: new LRU({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
+            fill: (args, signal) => this.readChunk(args, { signal }),
         });
     }
     /**
-     * @param {string} refName name of the reference sequence
-     * @param {number} start start of the region (in 0-based half-open coordinates)
-     * @param {number} end end of the region (in 0-based half-open coordinates)
-     * @param {function|object} lineCallback callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
-     * @returns {Promise} resolved when the whole read is finished, rejected on error
+     * @param refName name of the reference sequence
+     * @param start start of the region (in 0-based half-open coordinates)
+     * @param end end of the region (in 0-based half-open coordinates)
+     * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
+     * @returns promise that is resolved when the whole read is finished, rejected on error
      */
     async getLines(refName, start, end, opts) {
         let signal;
@@ -135,7 +130,7 @@ export default class TabixIndexedFile {
         for (let chunkNum = 0; chunkNum < chunks.length; chunkNum += 1) {
             let previousStartCoordinate;
             const c = chunks[chunkNum];
-            const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
+            const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c);
             checkAbortSignal(signal);
             let blockStart = 0;
             let pos = 0;
@@ -182,7 +177,7 @@ export default class TabixIndexedFile {
                     return;
                 }
                 // yield if we have emitted beyond the yield limit
-                if (last - Date.now() > 500) {
+                if (this.yieldTime && last - Date.now() > this.yieldTime) {
                     last = Date.now();
                     checkAbortSignal(signal);
                     await timeout(1);
@@ -198,15 +193,11 @@ 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
-     *
-     * @returns {Promise} for a buffer
      */
     async getHeaderBuffer(opts = {}) {
         const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
         checkAbortSignal(opts.signal);
-        const maxFetch = firstDataLine && firstDataLine.blockPosition
-            ? firstDataLine.blockPosition + maxBlockSize
-            : maxBlockSize;
+        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
         let bytes = await this._readRegion(0, maxFetch, opts);
@@ -234,7 +225,7 @@ export default class TabixIndexedFile {
                     lastNewline = i;
                 }
             }
-            bytes = bytes.slice(0, lastNewline + 1);
+            bytes = bytes.subarray(0, lastNewline + 1);
         }
         return bytes;
     }
@@ -246,16 +237,12 @@ export default class TabixIndexedFile {
      */
     async getHeader(opts = {}) {
         const bytes = await this.getHeaderBuffer(opts);
-        checkAbortSignal(opts.signal);
         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.
-     *
-     * @returns {Promise} for an array of string sequence names
+     * they occur in the file. reference sequence renaming is not applied
+     * to these names.
      */
     async getReferenceSequenceNames(opts = {}) {
         const metadata = await this.getMetadata(opts);
@@ -271,7 +258,8 @@ export default class TabixIndexedFile {
      * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
      * true if line is a data line that overlaps the given region
      */
-    checkLine({ columnNumbers, metaChar, coordinateType, format, }, regionRefName, regionStart, regionEnd, line) {
+    checkLine(metadata, regionRefName, regionStart, regionEnd, line) {
+        const { columnNumbers, metaChar, coordinateType, format } = metadata;
         // skip meta lines
         if (line.charAt(0) === metaChar) {
             return { overlaps: false };
@@ -376,31 +364,30 @@ export default class TabixIndexedFile {
     }
     /**
      * return the approximate number of data lines in the given reference sequence
-     * @param {string} refSeq reference sequence name
-     * @returns {Promise} for number of data lines present on that reference sequence
+     * @param refSeq reference sequence name
+     * @returns number of data lines present on that reference sequence
      */
     async lineCount(refName, opts = {}) {
         return this.index.lineCount(refName, opts);
     }
-    async _readRegion(position, compressedSize, opts = {}) {
-        const { bytesRead, buffer } = await this.filehandle.read(Buffer.alloc(compressedSize), 0, compressedSize, position, opts);
-        return bytesRead < compressedSize ? buffer.slice(0, bytesRead) : buffer;
+    async _readRegion(pos, size, opts = {}) {
+        const b = 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
-     * @param {Chunk} chunk
-     * @returns {Promise} for a string chunk of the file
      */
-    async readChunk(chunk, opts = {}) {
+    async readChunk(c, opts = {}) {
         // fetch the uncompressed data, uncompress carefully a block at a time,
         // and stop when done
-        const compressedData = await this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
+        const data = await this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
         try {
-            return unzipChunkSlice(compressedData, chunk);
+            return unzipChunkSlice(data, c);
         }
         catch (e) {
-            throw new Error(`error decompressing chunk ${chunk.toString()} ${e}`);
+            throw new Error(`error decompressing c ${c.toString()} ${e}`);
         }
     }
 }

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package/esm/tbi.d.ts

@@ -17,12 +17,12 @@ export default class TabixIndex extends IndexFile {
         metaChar: string | null;
         maxBinNumber: number;
         maxRefLength: number;
-        skipLines: any;
+        skipLines: number;
         firstDataLine: VirtualOffset | undefined;
         columnNumbers: {
-            ref: any;
-            start: any;
-            end: any;
+            ref: number;
+            start: number;
+            end: number;
         };
         coordinateType: string;
         format: string;

package/esm/tbi.js

@@ -38,10 +38,10 @@ export default class TabixIndex extends IndexFile {
         }
         return -1;
     }
-    // memoize
     // fetch and parse the index
     async _parse(opts = {}) {
-        const bytes = await unzip((await this.filehandle.readFile(opts)));
+        const buf = await this.filehandle.readFile(opts);
+        const bytes = await unzip(buf);
         checkAbortSignal(opts.signal);
         // check TBI magic numbers
         if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
@@ -74,7 +74,7 @@ export default class TabixIndex extends IndexFile {
         const skipLines = bytes.readInt32LE(28);
         // read sequence dictionary
         const nameSectionLength = bytes.readInt32LE(32);
-        const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
+        const { refNameToId, refIdToName } = this._parseNameBytes(bytes.subarray(36, 36 + nameSectionLength));
         // read the indexes for each reference sequence
         let currOffset = 36 + nameSectionLength;
         let firstDataLine;
@@ -139,7 +139,7 @@ export default class TabixIndex extends IndexFile {
         };
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
+        const lineCount = longToNumber(Long.fromBytesLE(bytes.subarray(offset + 16, offset + 24), true));
         return { lineCount };
     }
     _parseNameBytes(namesBytes) {

package/esm/tbi.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.6",
+  "version": "1.5.7",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -46,23 +46,23 @@
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^29.2.4",
+    "@types/jest": "^29.5.0",
     "@types/long": "^4.0.0",
-    "@types/node": "^18.0.6",
+    "@types/node": "^18.15.5",
     "@types/quick-lru": "2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.30.7",
-    "@typescript-eslint/parser": "^5.30.7",
-    "eslint": "^8.20.0",
-    "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-import": "^2.25.3",
+    "@typescript-eslint/eslint-plugin": "^5.56.0",
+    "@typescript-eslint/parser": "^5.56.0",
+    "eslint": "^8.36.0",
+    "eslint-config-prettier": "^8.8.0",
+    "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-prettier": "^4.2.1",
-    "jest": "^29.3.1",
-    "jest-environment-jsdom": "^29.3.1",
-    "prettier": "^2.7.1",
-    "rimraf": "^3.0.2",
+    "jest": "^29.5.0",
+    "jest-environment-jsdom": "^29.5.0",
+    "prettier": "^2.8.6",
+    "rimraf": "^4.4.1",
     "standard-changelog": "^2.0.27",
-    "ts-jest": "^29.0.3",
-    "typescript": "^4.7.4"
+    "ts-jest": "^29.0.5",
+    "typescript": "^5.0.2"
   },
   "publishConfig": {
     "access": "public"

package/src/csi.ts

@@ -45,25 +45,13 @@ export default class CSI extends IndexFile {
   }
   async indexCov() {
     throw new Error('CSI indexes do not support indexcov')
-    return []
   }
 
-  parseAuxData(bytes: Buffer, offset: number, auxLength: number) {
-    if (auxLength < 30) {
-      return {
-        refIdToName: [],
-        refNameToId: {},
-      }
-    }
-
+  parseAuxData(bytes: Buffer, offset: number) {
     const formatFlags = bytes.readInt32LE(offset)
     const coordinateType =
       formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
-    const format = (
-      { 0: 'generic', 1: 'SAM', 2: 'VCF' } as {
-        [key: number]: string
-      }
-    )[formatFlags & 0xf]
+    const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf]
     if (!format) {
       throw new Error(`invalid Tabix preset format flags ${formatFlags}`)
     }
@@ -73,12 +61,12 @@ export default class CSI extends IndexFile {
       end: bytes.readInt32LE(offset + 12),
     }
     const metaValue = bytes.readInt32LE(offset + 16)
-    const metaChar = metaValue ? String.fromCharCode(metaValue) : ''
+    const metaChar = metaValue ? String.fromCharCode(metaValue) : null
     const skipLines = bytes.readInt32LE(offset + 20)
     const nameSectionLength = bytes.readInt32LE(offset + 24)
 
     const { refIdToName, refNameToId } = this._parseNameBytes(
-      bytes.slice(offset + 28, offset + 28 + nameSectionLength),
+      bytes.subarray(offset + 28, offset + 28 + nameSectionLength),
     )
 
     return {
@@ -132,18 +120,18 @@ export default class CSI extends IndexFile {
     this.depth = bytes.readInt32LE(8)
     this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7
     const maxRefLength = 2 ** (this.minShift + this.depth * 3)
-
     const auxLength = bytes.readInt32LE(12)
-    let aux: {
-      refIdToName: string[]
-      refNameToId: { [key: string]: number }
-    } = {
-      refIdToName: [],
-      refNameToId: {},
-    }
-    if (auxLength) {
-      aux = this.parseAuxData(bytes, 16, auxLength)
-    }
+    const aux =
+      auxLength && auxLength >= 30
+        ? this.parseAuxData(bytes, 16)
+        : {
+            refIdToName: [],
+            refNameToId: {},
+            metaChar: null,
+            columnNumbers: { ref: 0, start: 1, end: 2 },
+            coordinateType: 'zero-based-half-open',
+            format: 'generic',
+          }
     const refCount = bytes.readInt32LE(16 + auxLength)
 
     // read the indexes for each reference sequence
@@ -199,7 +187,7 @@ export default class CSI extends IndexFile {
   parsePseudoBin(bytes: Buffer, offset: number) {
     const lineCount = longToNumber(
       Long.fromBytesLE(
-        Array.prototype.slice.call(bytes, offset + 28, offset + 36),
+        bytes.subarray(offset + 28, offset + 36) as unknown as number[],
         true,
       ),
     )

package/src/indexFile.ts

@@ -1,5 +1,3 @@
-import AbortablePromiseCache from 'abortable-promise-cache'
-import QuickLRU from 'quick-lru'
 import { GenericFilehandle } from 'generic-filehandle'
 import VirtualOffset from './virtualOffset'
 import Chunk from './chunk'
@@ -10,15 +8,21 @@ export interface Options {
   signal?: AbortSignal
 }
 
+export interface IndexData {
+  refNameToId: { [key: string]: number }
+  refIdToName: string[]
+  metaChar: string | null
+  columnNumbers: { ref: number; start: number; end: number }
+  coordinateType: string
+  format: string
+  [key: string]: any
+}
+
 export default abstract class IndexFile {
   public filehandle: GenericFilehandle
   public renameRefSeq: (arg0: string) => string
-  private _parseCache: any
+  private parseP?: Promise<IndexData>
 
-  /**
-   * @param {filehandle} filehandle
-   * @param {function} [renameRefSeqs]
-   */
   constructor({
     filehandle,
     renameRefSeqs = (n: string) => n,
@@ -32,10 +36,7 @@ export default abstract class IndexFile {
 
   public abstract lineCount(refName: string, args: Options): Promise<number>
 
-  protected abstract _parse(opts: Options): Promise<{
-    refNameToId: { [key: string]: number }
-    refIdToName: string[]
-  }>
+  protected abstract _parse(opts: Options): Promise<IndexData>
 
   public async getMetadata(opts: Options = {}) {
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
@@ -64,13 +65,13 @@ export default abstract class IndexFile {
   }
 
   async parse(opts: Options = {}) {
-    if (!this._parseCache) {
-      this._parseCache = new AbortablePromiseCache({
-        cache: new QuickLRU({ maxSize: 1 }),
-        fill: () => this._parse(opts),
+    if (!this.parseP) {
+      this.parseP = this._parse(opts).catch(e => {
+        this.parseP = undefined
+        throw e
       })
     }
-    return this._parseCache.get('index', null, undefined)
+    return this.parseP
   }
 
   async hasRefSeq(seqId: number, opts: Options = {}) {