@gmod/tabix 3.3.9 → 3.4.1

package/esm/tabixIndexedFile.js.map

@@ -1 +1 @@
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package/esm/tbi.d.ts

@@ -3,6 +3,7 @@ import IndexFile from './indexFile.ts';
 import type { Options, RefIndex } from './indexFile.ts';
 import type VirtualOffset from './virtualOffset.ts';
 export default class TabixIndex extends IndexFile {
+    /** @internal */
     _parse(opts?: Options): Promise<{
         indices: (refId: number) => RefIndex | undefined;
         metaChar: string | undefined;

package/esm/tbi.js

@@ -21,9 +21,12 @@ function reg2bins(beg, end) {
     ];
 }
 export default class TabixIndex extends IndexFile {
-    // fetch and parse the index
+    /** @internal */
     async _parse(opts = {}) {
-        const buf = await this.filehandle.readFile({ signal: opts.signal });
+        const buf = await this.filehandle.readFile({
+            signal: opts.signal,
+            onProgress: opts.onProgress,
+        });
         const bytes = (await unzip(buf));
         const dataView = new DataView(bytes.buffer);
         if (dataView.getUint32(0, true) !== TBI_MAGIC) {

package/esm/tbi.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.3.9",
+  "version": "3.4.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
   "main": "dist/index.js",
@@ -37,7 +37,7 @@
     "build": "pnpm build:esm && pnpm build:es5",
     "benchonly": "vitest bench",
     "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
-    "docs": "documentation readme --shallow src/tabixIndexedFile.ts --section TabixIndexedFile",
+    "build:docs": "typedoc && node scripts/build-docs.mjs",
     "postbuild": "webpack",
     "prepublishOnly": "pnpm lint && pnpm test run && pnpm build",
     "version": "standard-changelog && git add CHANGELOG.md"
@@ -51,22 +51,23 @@
     "@gmod/abortable-promise-cache": "^3.0.4",
     "@gmod/bgzf-filehandle": "^6.2.0",
     "@jbrowse/quick-lru": "^7.3.5",
-    "generic-filehandle2": "^2.1.10"
+    "generic-filehandle2": "^2.2.0"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",
-    "@types/node": "^25.9.1",
-    "@vitest/coverage-v8": "^4.1.8",
-    "documentation": "^14.0.3",
-    "eslint": "^10.4.1",
+    "@types/node": "^25.9.3",
+    "@vitest/coverage-v8": "^4.1.9",
+    "eslint": "^10.5.0",
     "eslint-plugin-import-x": "^4.16.2",
     "eslint-plugin-unicorn": "^64.0.0",
-    "prettier": "^3.8.3",
+    "prettier": "^3.8.4",
     "rimraf": "^6.1.3",
     "standard-changelog": "^7.0.1",
+    "typedoc": "^0.28.19",
+    "typedoc-plugin-markdown": "^4.12.0",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.60.0",
-    "vitest": "^4.1.8",
+    "typescript-eslint": "^8.61.1",
+    "vitest": "^4.1.9",
     "webpack": "^5.107.2",
     "webpack-cli": "^7.0.3"
   },

package/src/csi.ts

@@ -37,12 +37,17 @@ export default class CSI extends IndexFile {
     this.depth = 0
     this.minShift = 0
   }
+  /** @internal */
   indexCov() {
     throw new Error('CSI indexes do not support indexcov')
   }
 
+  /** @internal */
   async _parse(opts: Options = {}) {
-    const buf = await this.filehandle.readFile({ signal: opts.signal })
+    const buf = await this.filehandle.readFile({
+      signal: opts.signal,
+      onProgress: opts.onProgress,
+    })
     const bytes = (await unzip(buf)) as Uint8Array
     const dataView = new DataView(bytes.buffer)
 
@@ -187,9 +192,7 @@ export default class CSI extends IndexFile {
     return optimizeChunks(chunks)
   }
 
-  /**
-   * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-   */
+  /** @internal */
   reg2bins(beg: number, end: number) {
     const maxPos = 2 ** (this.minShift + this.depth * 3)
     if (end > maxPos) {

package/src/indexFile.ts

@@ -4,6 +4,12 @@ import type { GenericFilehandle } from 'generic-filehandle2'
 
 export interface Options {
   signal?: AbortSignal
+  /**
+   * Called as the index (.tbi/.csi) is downloaded, with cumulative downloaded
+   * bytes and the total. The index is a whole-file read, so this streams real
+   * byte progress. Lets callers show a determinate "downloading index" bar.
+   */
+  onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
 }
 
 export interface RefIndex {
@@ -41,6 +47,7 @@ export default abstract class IndexFile {
 
   protected abstract _parse(opts: Options): Promise<IndexData>
 
+  /** @internal */
   public async lineCount(refName: string, opts: Options = {}) {
     const indexData = await this.parse(opts)
     const refId = indexData.refNameToId[refName]
@@ -50,11 +57,13 @@ export default abstract class IndexFile {
     return indexData.indices(refId)?.stats?.lineCount ?? -1
   }
 
+  /** @internal */
   public async getMetadata(opts: Options = {}) {
     const { indices: _indices, ...rest } = await this.parse(opts)
     return rest
   }
 
+  /** @internal */
   public abstract blocksForRange(
     refName: string,
     start: number,
@@ -62,6 +71,7 @@ export default abstract class IndexFile {
     opts: Options,
   ): Promise<Chunk[]>
 
+  /** @internal */
   async parse(opts: Options = {}) {
     this.parseP ??= this._parse(opts).catch((error: unknown) => {
       this.parseP = undefined
@@ -70,6 +80,7 @@ export default abstract class IndexFile {
     return this.parseP
   }
 
+  /** @internal */
   async hasRefSeq(seqId: number, opts: Options = {}) {
     const idx = await this.parse(opts)
     return !!idx.indices(seqId)?.binIndex

package/src/tabixIndexedFile.ts

@@ -26,6 +26,14 @@ type GetLinesCallback = (
 interface GetLinesOpts {
   signal?: AbortSignal
   lineCallback: GetLinesCallback
+  /**
+   * Called as the compressed data blocks covering the query are fetched, with
+   * cumulative downloaded bytes and the total bytes to fetch. Reported at block
+   * granularity (one tick per chunk, including instant ticks for cache hits),
+   * which is the natural unit since chunk byte sizes are known up front from
+   * the index. Lets callers render a determinate download progress bar.
+   */
+  onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
 }
 
 interface ReadChunk {
@@ -132,24 +140,14 @@ function parseIntFromBytes(buffer: Uint8Array, start: number, end: number) {
   return val
 }
 
+/**
+ * Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
+ */
 export default class TabixIndexedFile {
   private filehandle: GenericFilehandle
   private index: IndexFile
   private chunkCache: AbortablePromiseCache<Chunk, ReadChunk>
 
-  /**
-   * @param {object} args
-   * @param {string} [args.path]
-   * @param {object} [args.filehandle]
-   * @param {string} [args.url]
-   * @param {string} [args.tbiPath]
-   * @param {string} [args.tbiUrl]
-   * @param {object} [args.tbiFilehandle]
-   * @param {string} [args.csiPath]
-   * @param {string} [args.csiUrl]
-   * @param {object} [args.csiFilehandle]
-   * @param {number} [args.chunkCacheSize]
-   */
   constructor({
     path,
     filehandle,
@@ -228,11 +226,10 @@ export default class TabixIndexedFile {
   }
 
   /**
-   * @param {string} refName name of the reference sequence
-   * @param {number|undefined} start start of the region (0-based half-open)
-   * @param {number|undefined} end end of the region (0-based half-open)
-   * @param {GetLinesOpts|GetLinesCallback} opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
-   * @returns {Promise} promise that is resolved when the whole read is finished, rejected on error
+   * @param refName name of the reference sequence
+   * @param s start of the region (0-based half-open)
+   * @param e end of the region (0-based half-open)
+   * @param opts callback invoked for each line, or an options object with `lineCallback` and optional `signal`
    */
   async getLines(
     refName: string,
@@ -243,6 +240,7 @@ export default class TabixIndexedFile {
     let signal: AbortSignal | undefined
     let options: Options = {}
     let callback: GetLinesCallback
+    let onProgress: GetLinesOpts['onProgress']
 
     if (typeof opts === 'function') {
       callback = opts
@@ -250,6 +248,7 @@ export default class TabixIndexedFile {
       options = opts
       callback = opts.lineCallback
       signal = opts.signal
+      onProgress = opts.onProgress
     }
 
     const metadata = await this.index.getMetadata(options)
@@ -282,12 +281,21 @@ export default class TabixIndexedFile {
     // the sentinel tabs[0] = blockStart - 1, column N spans tabs[N-1]+1..tabs[N]
     const tabs = new Int32Array(maxColumn + 1)
 
+    let totalBytes = 0
+    for (const c of chunks) {
+      totalBytes += c.fetchedSize()
+    }
+    let downloadedBytes = 0
+    onProgress?.(0, totalBytes)
+
     for (const c of chunks) {
       const { buffer, cpositions, dpositions } = await this.chunkCache.get(
         c.toString(),
         c,
         signal,
       )
+      downloadedBytes += c.fetchedSize()
+      onProgress?.(downloadedBytes, totalBytes)
       const minvDataPosition = c.minv.dataPosition
 
       let blockStart = 0
@@ -391,6 +399,7 @@ export default class TabixIndexedFile {
     }
   }
 
+  /** @internal */
   async getMetadata(opts: Options = {}) {
     return this.index.getMetadata(opts)
   }
@@ -435,15 +444,12 @@ export default class TabixIndexedFile {
     return metadata.refIdToName
   }
 
-  /**
-   * return the number of data lines in the given reference sequence
-   * @param {string} refName reference sequence name
-   * @returns {number} number of data lines present on that reference sequence
-   */
+  /** @param refName reference sequence name */
   async lineCount(refName: string, opts: Options = {}) {
     return this.index.lineCount(refName, opts)
   }
 
+  /** @internal */
   async readChunk(c: Chunk, opts: Options = {}) {
     const ret = await this.filehandle.read(
       c.fetchedSize(),

package/src/tbi.ts

@@ -34,9 +34,12 @@ function reg2bins(beg: number, end: number) {
 }
 
 export default class TabixIndex extends IndexFile {
-  // fetch and parse the index
+  /** @internal */
   async _parse(opts: Options = {}) {
-    const buf = await this.filehandle.readFile({ signal: opts.signal })
+    const buf = await this.filehandle.readFile({
+      signal: opts.signal,
+      onProgress: opts.onProgress,
+    })
     const bytes = (await unzip(buf)) as Uint8Array
     const dataView = new DataView(bytes.buffer)