@gmod/tabix 3.3.9 → 3.4.0

package/README.md

@@ -7,280 +7,125 @@ Read Tabix-indexed files using either .tbi or .csi indexes.
 
 ## Install
 
-    $ npm install @gmod/tabix
+```bash
+npm install @gmod/tabix
+```
 
 ## Usage
 
-### Importing the module
-
 ```typescript
 import { TabixIndexedFile } from '@gmod/tabix'
-```
 
-### Single file bundle
+// Local file — TBI index assumed at path + '.tbi'
+const file = new TabixIndexedFile({ path: 'file.vcf.gz' })
 
-You can use tabix-js without NPM also with the tabix-bundle.js. See the example
-directory for usage with script tag [example/index.html](example/index.html)
-
-```html
-<script src="https://unpkg.com/@gmod/tabix/dist/tabix-bundle.js"></script>
-```
+// CSI index
+const file = new TabixIndexedFile({
+  path: 'file.vcf.gz',
+  csiPath: 'file.vcf.gz.csi',
+})
 
-### TabixIndexedFile constructor
+// Remote files
+const file = new TabixIndexedFile({
+  url: 'https://example.com/file.vcf.gz',
+  tbiUrl: 'https://example.com/file.vcf.gz.tbi',
+})
 
-Basic usage of TabixIndexedFile under node.js supplies a path and optionally a
-tbiPath to the constructor. If no tbiPath is supplied, it assumes that the
-path+'.tbi' is the location of the tbiPath.
+// Or with a filehandle from generic-filehandle2
+import { RemoteFile } from 'generic-filehandle2'
 
-```typescript
-const tbiIndexed = new TabixIndexedFile({
-  path: 'path/to/my/file.gz',
-  tbiPath: 'path/to/my/file.gz.tbi',
+const file = new TabixIndexedFile({
+  filehandle: new RemoteFile('https://example.com/file.vcf.gz'),
+  tbiFilehandle: new RemoteFile('https://example.com/file.vcf.gz.tbi'),
 })
 ```
 
-You can also use CSI indexes:
+### getLines
+
+Fetches lines overlapping a region. `start`/`end` are 0-based half-open coordinates (unlike the tabix CLI which uses 1-based closed).
 
 ```typescript
-const csiIndexed = new TabixIndexedFile({
-  path: 'path/to/my/file.gz',
-  csiPath: 'path/to/my/file.gz.csi',
-})
+const lines: string[] = []
+await file.getLines('chr1', 200, 300, line => lines.push(line))
 ```
 
-#### TabixIndexedFile constructor with remote files
+The callback also receives the virtual file offset and parsed coordinates for the line:
 
 ```typescript
-const remoteTbiIndexed = new TabixIndexedFile({
-  url: 'http://yourhost/file.vcf.gz',
-  tbiUrl: 'http://yourhost/file.vcf.gz.tbi', // can also be csiUrl
+await file.getLines('chr1', 200, 300, (line, fileOffset, start, end) => {
+  lines.push(line)
 })
 ```
 
-You can also supply a filehandle-like object from
-[generic-filehandle2](https://github.com/GMOD/generic-filehandle2):
+Pass an options object to use an `AbortSignal`:
 
 ```typescript
-import { RemoteFile } from 'generic-filehandle2'
-
-const remoteTbiIndexed = new TabixIndexedFile({
-  filehandle: new RemoteFile('http://yourhost/file.vcf.gz'),
-  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi'), // can also be csiFilehandle
+const aborter = new AbortController()
+await file.getLines('chr1', 200, 300, {
+  lineCallback: (line, fileOffset, start, end) => lines.push(line),
+  signal: aborter.signal,
 })
 ```
 
-### getLines
-
-The basic function this module provides is just called `getLines` and it returns
-text contents from the tabix file (it unzips the bgzipped data) and supplies it
-to a callback that you provide one line at a time.
+Notes:
+- Meta/comment lines are skipped
+- Line strings have no trailing whitespace
+- Pass `undefined` for `end` to read to the end of the contig
 
-Important: the `start` and `end` values that are supplied to `getLines` are
-0-based half-open coordinates. This is different from the 1-based values that
-are supplied to the tabix command line tool
+### Without NPM (CDN)
 
-```typescript
-const lines = []
-await tbiIndexed.getLines(
-  'ctgA',
-  200,
-  300,
-  function (line, fileOffset, start, end) {
-    lines.push(line)
-  },
-)
+```html
+<script src="https://unpkg.com/@gmod/tabix/dist/tabix-bundle.js"></script>
 ```
 
-After running this, `lines` contains the matching lines from the file. The
-callback receives:
+See [example/index.html](example/index.html) for a working demo.
 
-- `line` — the raw line string
-- `fileOffset` — virtual file offset, useful as a unique line identifier
-- `start` / `end` — the parsed coordinates of that line (0-based half-open)
+## API
 
-You can also pass an options object instead of a bare callback:
+### `new TabixIndexedFile(args)`
 
-```typescript
-const lines = []
-const aborter = new AbortController()
-await tbiIndexed.getLines('ctgA', 200, 300, {
-  lineCallback: (line, fileOffset, start, end) => lines.push(line),
-  signal: aborter.signal, // an optional AbortSignal from an AbortController
-})
-```
-
-Notes about the returned values of `getLines`:
+| Arg | Type | Description |
+| --- | --- | --- |
+| `path` | `string?` | Local file path |
+| `url` | `string?` | Remote URL |
+| `filehandle` | `GenericFilehandle?` | Custom filehandle (from [generic-filehandle2](https://github.com/GMOD/generic-filehandle2)) |
+| `tbiPath` | `string?` | TBI index path (defaults to `path + '.tbi'`) |
+| `tbiUrl` | `string?` | TBI index URL |
+| `tbiFilehandle` | `GenericFilehandle?` | TBI index filehandle |
+| `csiPath` | `string?` | CSI index path |
+| `csiUrl` | `string?` | CSI index URL |
+| `csiFilehandle` | `GenericFilehandle?` | CSI index filehandle |
+| `chunkCacheSize` | `number?` | Chunk LRU cache size in bytes (default 5 MiB) |
 
-- commented (meta) lines are skipped.
-- line strings do not include any trailing whitespace characters.
-- if `getLines` is called with an undefined `end` parameter it gets all lines
-  from start going to the end of the contig e.g.
+### `getLines(refName, start, end, opts)`
 
-```typescript
-const lines = []
-await tbiIndexed.getLines('ctgA', 0, undefined, line => lines.push(line))
-console.log(lines)
-```
+Calls `opts` (or `opts.lineCallback`) for each line overlapping `[start, end)`.
 
-## API (auto-generated)
-
-### TabixIndexedFile
-
-##### Table of Contents
-
-- [constructor](#constructor)
-  - [Parameters](#parameters)
-- [getLines](#getlines)
-  - [Parameters](#parameters-1)
-- [getHeaderBuffer](#getheaderbuffer)
-  - [Parameters](#parameters-2)
-- [getHeader](#getheader)
-  - [Parameters](#parameters-3)
-- [getReferenceSequenceNames](#getreferencesequencenames)
-  - [Parameters](#parameters-4)
-- [checkLine](#checkline)
-  - [Parameters](#parameters-5)
-- [lineCount](#linecount)
-  - [Parameters](#parameters-6)
-- [readChunk](#readchunk)
-  - [Parameters](#parameters-7)
-
-#### constructor
-
-##### Parameters
-
-- `args`
-  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;
-  - `args.path`
-    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
-  - `args.filehandle` **filehandle?**&#x20;
-  - `args.url`
-    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
-  - `args.tbiPath`
-    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
-  - `args.tbiUrl` **tbiUrl?**&#x20;
-  - `args.tbiFilehandle` **filehandle?**&#x20;
-  - `args.csiPath`
-    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
-  - `args.csiUrl` **csiUrl?**&#x20;
-  - `args.csiFilehandle` **filehandle?**&#x20;
-  - `args.yieldTime`
-    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?**
-    yield to main thread after N milliseconds if reading features is taking a
-    long time to avoid hanging main thread (optional, default `500`)
-  - `args.renameRefSeqs`
-    **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?**
-    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. (optional, default `n=>n`)
-  - `args.chunkCacheSize` (optional, default `5*2**20`)
-
-#### getLines
-
-##### Parameters
-
-- `refName`
-  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
-  name of the reference sequence
-- `start`
-  **([number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
-  |
-  [undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined))**
-  start of the region (0-based half-open)
-- `end`
-  **([number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
-  |
-  [undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined))**
-  end of the region (0-based half-open)
-- `opts` **(GetLinesOpts | GetLinesCallback)** callback invoked for each line,
-  or an options object with `lineCallback` and optional `signal`
-
-Returns **any** promise that is resolved when the whole read is finished,
-rejected on error
-
-#### getHeaderBuffer
-
-get a buffer containing the "header" region of the file, which are the bytes up
-to the first non-meta line
-
-##### Parameters
-
-- `opts` **Options** (optional, default `{}`)
-
-#### getHeader
-
-get a string containing the "header" region of the file, is the portion up to
-the first non-meta line
-
-##### Parameters
-
-- `opts` **Options** (optional, default `{}`)
-
-Returns
-**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)**
-for a string
-
-#### getReferenceSequenceNames
-
-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.
-
-##### Parameters
-
-- `opts` **Options** (optional, default `{}`)
-
-#### checkLine
-
-##### Parameters
-
-- `metadata`
-  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
-  metadata object from the parsed index, containing columnNumbers, metaChar, and
-  format
-- `regionRefName`
-  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**&#x20;
-- `regionStart`
-  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-  region start coordinate (0-based-half-open)
-- `regionEnd`
-  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
-  region end coordinate (0-based-half-open)
-- `line`
-  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**&#x20;
+Callback signature: `(line: string, fileOffset: number, start: number, end: number) => void`
 
-Returns
-**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
-like `{startCoordinate, overlaps}`. overlaps is boolean, true if line is a data
-line that overlaps the given region
+### `getHeader(opts?): Promise<string>`
 
-#### lineCount
+Returns all comment/meta lines before the first data line as a string.
 
-return the number of data lines in the given reference sequence
+### `getHeaderBuffer(opts?): Promise<Uint8Array>`
 
-##### Parameters
+Returns the header as raw bytes.
 
-- `refName`
-  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
-  reference sequence name
-- `opts` **Options** (optional, default `{}`)
+### `getReferenceSequenceNames(opts?): Promise<string[]>`
 
-Returns **any** number of data lines present on that reference sequence
+Returns reference sequence names in index order. `renameRefSeqs` is not applied to these names.
 
-#### readChunk
+### `lineCount(refName, opts?): Promise<number>`
 
-read and uncompress the data in a chunk (composed of one or more contiguous
-bgzip blocks) of the file
+Returns the number of data lines on the given reference, or `-1` if the reference is not in the index.
 
-##### Parameters
+### `bytesForRegions(regions, opts?): Promise<number>`
 
-- `c` **Chunk**&#x20;
-- `opts` **Options** (optional, default `{}`)
+Estimates the compressed byte size of index chunks covering the given regions. Useful for deciding whether a request is too large before calling `getLines`.
 
 ## Publishing
 
-[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
-Actions.
+[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub Actions.
 
 ```bash
 pnpm version patch  # or minor/major
@@ -288,10 +133,7 @@ pnpm version patch  # or minor/major
 
 ## Academic Use
 
-This package was written with funding from the [NHGRI](http://genome.gov) as
-part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
-project that you publish, please cite the most recent JBrowse paper, which will
-be linked from [jbrowse.org](http://jbrowse.org).
+This package was written with funding from the [NHGRI](http://genome.gov) as part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from [jbrowse.org](http://jbrowse.org).
 
 ## License
 

package/dist/csi.d.ts

@@ -10,7 +10,9 @@ export default class CSI extends IndexFile {
     constructor(args: {
         filehandle: GenericFilehandle;
     });
+    /** @internal */
     indexCov(): void;
+    /** @internal */
     _parse(opts?: Options): Promise<{
         csi: boolean;
         refCount: number;
@@ -54,8 +56,6 @@ export default class CSI extends IndexFile {
         format: string;
     }>;
     blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     */
+    /** @internal */
     reg2bins(beg: number, end: number): (readonly [number, number])[];
 }

package/dist/csi.js

@@ -28,9 +28,11 @@ class CSI extends indexFile_ts_1.default {
         this.depth = 0;
         this.minShift = 0;
     }
+    /** @internal */
     indexCov() {
         throw new Error('CSI indexes do not support indexcov');
     }
+    /** @internal */
     async _parse(opts = {}) {
         const buf = await this.filehandle.readFile({ signal: opts.signal });
         const bytes = (await (0, bgzf_filehandle_1.unzip)(buf));
@@ -159,9 +161,7 @@ class CSI extends indexFile_ts_1.default {
         }
         return (0, util_ts_1.optimizeChunks)(chunks);
     }
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     */
+    /** @internal */
     reg2bins(beg, end) {
         const maxPos = 2 ** (this.minShift + this.depth * 3);
         if (end > maxPos) {

package/dist/csi.js.map

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

@@ -40,7 +40,9 @@ export default abstract class IndexFile {
         filehandle: GenericFilehandle;
     });
     protected abstract _parse(opts: Options): Promise<IndexData>;
+    /** @internal */
     lineCount(refName: string, opts?: Options): Promise<number>;
+    /** @internal */
     getMetadata(opts?: Options): Promise<{
         refNameToId: Record<string, number>;
         refIdToName: string[];
@@ -62,7 +64,10 @@ export default abstract class IndexFile {
         csiVersion?: number;
         depth?: number;
     }>;
+    /** @internal */
     abstract blocksForRange(refName: string, start: number, end: number, opts: Options): Promise<Chunk[]>;
+    /** @internal */
     parse(opts?: Options): Promise<IndexData>;
+    /** @internal */
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
 }

package/dist/indexFile.js

@@ -6,6 +6,7 @@ class IndexFile {
     constructor({ filehandle }) {
         this.filehandle = filehandle;
     }
+    /** @internal */
     async lineCount(refName, opts = {}) {
         const indexData = await this.parse(opts);
         const refId = indexData.refNameToId[refName];
@@ -14,10 +15,12 @@ class IndexFile {
         }
         return indexData.indices(refId)?.stats?.lineCount ?? -1;
     }
+    /** @internal */
     async getMetadata(opts = {}) {
         const { indices: _indices, ...rest } = await this.parse(opts);
         return rest;
     }
+    /** @internal */
     async parse(opts = {}) {
         this.parseP ??= this._parse(opts).catch((error) => {
             this.parseP = undefined;
@@ -25,6 +28,7 @@ class IndexFile {
         });
         return this.parseP;
     }
+    /** @internal */
     async hasRefSeq(seqId, opts = {}) {
         const idx = await this.parse(opts);
         return !!idx.indices(seqId)?.binIndex;

package/dist/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAiCA,MAA8B,SAAS;IAC9B,UAAU,CAAmB;IAC5B,MAAM,CAAqB;IAEnC,YAAY,EAAE,UAAU,EAAqC;QAC3D,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;IAC9B,CAAC;IAID,gBAAgB;IACT,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACxD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACzD,CAAC;IAED,gBAAgB;IACT,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IAUD,gBAAgB;IAChB,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;YACzD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,MAAM,KAAK,CAAA;QACb,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF;AAhDD,4BAgDC"}