@gmod/tabix 1.5.15 → 1.6.1

package/esm/tabixIndexedFile.js

@@ -6,10 +6,11 @@ import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
 import { checkAbortSignal } from './util';
 import TBI from './tbi';
 import CSI from './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;
 export default class TabixIndexedFile {
     /**
      * @param {object} args
@@ -26,15 +27,18 @@ 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 = 500, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
         if (filehandle) {
             this.filehandle = filehandle;
         }
@@ -96,7 +100,6 @@ export default class TabixIndexedFile {
             throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
         }
         this.renameRefSeq = renameRefSeqs;
-        this.yieldTime = yieldTime;
         this.chunkCache = new AbortablePromiseCache({
             cache: new LRU({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
             fill: (args, signal) => this.readChunk(args, { signal }),
@@ -116,7 +119,7 @@ export default class TabixIndexedFile {
      * rejected on error
      */
     async getLines(refName, s, e, opts) {
-        var _a;
+        var _a, _b;
         let signal;
         let options = {};
         let callback;
@@ -141,20 +144,34 @@ export default class TabixIndexedFile {
         const chunks = await this.index.blocksForRange(refName, start, end, options);
         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 } = await this.chunkCache.get(c.toString(), c, signal);
             checkAbortSignal(signal);
             let blockStart = 0;
             let pos = 0;
-            while (blockStart < buffer.length) {
-                const n = buffer.indexOf('\n', blockStart);
-                if (n === -1) {
-                    break;
+            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;
+                    }
+                    line = str.slice(blockStart, n);
+                }
+                else {
+                    n = buffer.indexOf('\n', 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();
                 }
-                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++]) { }
@@ -162,41 +179,30 @@ export default class TabixIndexedFile {
                 }
                 // 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
+                    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
+                    // 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
+                    // 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
+                    // 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();
-                    checkAbortSignal(signal);
-                    await timeout(1);
-                }
                 blockStart = n + 1;
             }
         }
@@ -211,7 +217,6 @@ export default class TabixIndexedFile {
     async getHeaderBuffer(opts = {}) {
         const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
         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
@@ -231,7 +236,7 @@ export default class TabixIndexedFile {
                     lastNewline = i;
                 }
             }
-            return bytes.slice(0, lastNewline + 1);
+            return bytes.subarray(0, lastNewline + 1);
         }
         return bytes;
     }
@@ -296,12 +301,15 @@ export default 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) {
@@ -311,12 +319,18 @@ export default 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,
+                            };
                         }
                     }
                 }
@@ -327,9 +341,11 @@ export default 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;
@@ -339,7 +355,10 @@ export default class TabixIndexedFile {
                 }
             }
         }
-        return { startCoordinate, overlaps: true };
+        return {
+            startCoordinate,
+            overlaps: true,
+        };
     }
     _getVcfEnd(startCoordinate, refSeq, info) {
         let endCoordinate = startCoordinate + refSeq.length;
@@ -382,7 +401,7 @@ export default class TabixIndexedFile {
     async _readRegion(pos, size, opts = {}) {
         const b = Buffer.alloc(size);
         const { bytesRead, buffer } = await this.filehandle.read(b, 0, size, pos, opts);
-        return buffer.slice(0, bytesRead);
+        return buffer.subarray(0, bytesRead);
     }
     /**
      * read and uncompress the data in a chunk (composed of one or more

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.15",
+  "version": "1.6.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -23,10 +23,11 @@
     "test": "vitest",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "format": "prettier --write .",
+    "docs": "documentation readme --shallow src/tabixIndexedFile.ts --section TabixIndexedFile",
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean && npm run lint",
-    "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "build:esm": "tsc --outDir esm",
+    "build:es5": "tsc --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "postbuild": "webpack",
     "preversion": "npm run lint && npm test run && npm run build",
@@ -55,14 +56,15 @@
     "@typescript-eslint/parser": "^8.0.1",
     "@vitest/coverage-v8": "^2.0.5",
     "buffer": "^6.0.3",
+    "documentation": "^14.0.3",
     "eslint": "^9.9.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.0.1",
-    "eslint-plugin-unicorn": "^55.0.0",
+    "eslint-plugin-unicorn": "^56.0.0",
     "prettier": "^3.3.3",
     "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",
-    "typescript": "^5.3.3",
+    "typescript": "~5.6.0",
     "typescript-eslint": "^8.0.1",
     "vitest": "^2.0.5",
     "webpack": "^5.93.0",

package/src/chunk.ts

@@ -20,7 +20,6 @@ export default class Chunk {
   }
 
   toUniqueString() {
-     
     return `${this.minv}..${this.maxv} (bin ${
       this.bin
     }, fetchedSize ${this.fetchedSize()})`

package/src/tabixIndexedFile.ts

@@ -10,6 +10,11 @@ import Chunk from './chunk'
 import TBI from './tbi'
 import CSI from './csi'
 
+function isASCII(str: string) {
+  // eslint-disable-next-line no-control-regex
+  return /^[\u0000-\u007F]*$/.test(str)
+}
+
 type GetLinesCallback = (line: string, fileOffset: number) => void
 
 const decoder =
@@ -27,13 +32,9 @@ interface ReadChunk {
   dpositions: number[]
 }
 
-function timeout(time: number) {
-  return new Promise(resolve => setTimeout(resolve, time))
-}
 export default class TabixIndexedFile {
   private filehandle: GenericFilehandle
   private index: IndexFile
-  private yieldTime: number
   private renameRefSeq: (n: string) => string
   private chunkCache: AbortablePromiseCache<Chunk, ReadChunk>
 
@@ -52,8 +53,11 @@ 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
@@ -70,7 +74,6 @@ export default class TabixIndexedFile {
     csiPath,
     csiUrl,
     csiFilehandle,
-    yieldTime = 500,
     renameRefSeqs = n => n,
     chunkCacheSize = 5 * 2 ** 20,
   }: {
@@ -83,7 +86,6 @@ export default class TabixIndexedFile {
     csiPath?: string
     csiUrl?: string
     csiFilehandle?: GenericFilehandle
-    yieldTime?: number
     renameRefSeqs?: (n: string) => string
     chunkCacheSize?: number
   }) {
@@ -141,7 +143,6 @@ export default class TabixIndexedFile {
     }
 
     this.renameRefSeq = renameRefSeqs
-    this.yieldTime = yieldTime
     this.chunkCache = new AbortablePromiseCache<Chunk, ReadChunk>({
       cache: new LRU({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
       fill: (args: Chunk, signal?: AbortSignal) =>
@@ -197,9 +198,7 @@ export default class TabixIndexedFile {
     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: number | undefined
       const { buffer, cpositions, dpositions } = await this.chunkCache.get(
         c.toString(),
         c,
@@ -209,13 +208,29 @@ export default class TabixIndexedFile {
       checkAbortSignal(signal)
       let blockStart = 0
       let pos = 0
-      while (blockStart < buffer.length) {
-        const n = buffer.indexOf('\n', blockStart)
-        if (n === -1) {
-          break
+
+      const str = decoder?.decode(buffer) ?? 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 < 500_000_000 && isASCII(str)
+      while (blockStart < str.length) {
+        let line: string
+        let n: number
+        if (strIsASCII) {
+          n = str.indexOf('\n', blockStart)
+          if (n === -1) {
+            break
+          }
+          line = str.slice(blockStart, n)
+        } else {
+          n = buffer.indexOf('\n', blockStart)
+          if (n === -1) {
+            break
+          }
+          const b = buffer.slice(blockStart, n)
+          line = decoder?.decode(b) ?? b.toString()
         }
-        const b = buffer.slice(blockStart, n)
-        const line = decoder?.decode(b) ?? b.toString()
 
         // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (dpositions) {
@@ -232,48 +247,31 @@ export default class TabixIndexedFile {
           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
+            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
+            // 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
+            // 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
+          // 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()
-          checkAbortSignal(signal)
-          await timeout(1)
-        }
         blockStart = n + 1
       }
     }
@@ -290,9 +288,9 @@ export default class TabixIndexedFile {
   async getHeaderBuffer(opts: Options = {}) {
     const { firstDataLine, metaChar, maxBlockSize } =
       await this.getMetadata(opts)
+
     checkAbortSignal(opts.signal)
 
-    // eslint-disable-next-line @typescript-eslint/restrict-plus-operands
     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
@@ -314,7 +312,7 @@ export default class TabixIndexedFile {
           lastNewline = i
         }
       }
-      return bytes.slice(0, lastNewline + 1)
+      return bytes.subarray(0, lastNewline + 1)
     }
     return bytes
   }
@@ -391,14 +389,17 @@ export default 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) {
           startCoordinate = parseInt(line.slice(currentColumnStart, i), 10)
@@ -407,12 +408,18 @@ export default 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,
+              }
             }
           }
         } else if (format === 'VCF' && currentColumnNumber === 4) {
@@ -426,9 +433,11 @@ export default class TabixIndexedFile {
                   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
@@ -438,7 +447,10 @@ export default class TabixIndexedFile {
         }
       }
     }
-    return { startCoordinate, overlaps: true }
+    return {
+      startCoordinate,
+      overlaps: true,
+    }
   }
 
   _getVcfEnd(startCoordinate: number, refSeq: string, info: any) {
@@ -490,7 +502,7 @@ export default class TabixIndexedFile {
       opts,
     )
 
-    return buffer.slice(0, bytesRead)
+    return buffer.subarray(0, bytesRead)
   }
 
   /**