@gmod/tabix 3.5.1 → 3.5.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +46 -19
- package/dist/csi.js +1 -1
- package/dist/csi.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.d.ts +17 -0
- package/dist/tabixIndexedFile.js +107 -3
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.js +12 -15
- package/dist/tbi.js.map +1 -1
- package/dist/util.d.ts +11 -2
- package/dist/util.js +31 -5
- package/dist/util.js.map +1 -1
- package/esm/csi.js +2 -2
- package/esm/csi.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +17 -0
- package/esm/tabixIndexedFile.js +107 -3
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.js +13 -16
- package/esm/tbi.js.map +1 -1
- package/esm/util.d.ts +11 -2
- package/esm/util.js +30 -4
- package/esm/util.js.map +1 -1
- package/package.json +4 -7
- package/src/csi.ts +2 -2
- package/src/tabixIndexedFile.ts +146 -3
- package/src/tbi.ts +13 -14
- package/src/util.ts +35 -8
package/README.md
CHANGED
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@@ -20,13 +20,13 @@ import { TabixIndexedFile } from '@gmod/tabix'
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const file = new TabixIndexedFile({ path: 'file.vcf.gz' })
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// CSI index
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-
const
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const csi = new TabixIndexedFile({
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path: 'file.vcf.gz',
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csiPath: 'file.vcf.gz.csi',
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})
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// Remote files
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const
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const remote = new TabixIndexedFile({
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url: 'https://example.com/file.vcf.gz',
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tbiUrl: 'https://example.com/file.vcf.gz.tbi',
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})
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@@ -34,7 +34,7 @@ const file = new TabixIndexedFile({
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// Or with a filehandle from generic-filehandle2
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import { RemoteFile } from 'generic-filehandle2'
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const
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const custom = new TabixIndexedFile({
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filehandle: new RemoteFile('https://example.com/file.vcf.gz'),
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tbiFilehandle: new RemoteFile('https://example.com/file.vcf.gz.tbi'),
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})
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@@ -59,21 +59,34 @@ await file.getLines('chr1', 200, 300, (line, fileOffset, start, end) => {
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})
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```
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Pass an options object to
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Pass an options object instead of a bare callback to abort the query or track
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download progress:
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```typescript
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const aborter = new AbortController()
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await file.getLines('chr1', 200, 300, {
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lineCallback: (line, fileOffset, start, end) => lines.push(line),
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signal: aborter.signal,
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onProgress: (bytesDownloaded, totalBytes) => {
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console.log(`${bytesDownloaded}/${totalBytes}`)
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},
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})
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```
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`onProgress` ticks once per compressed block, including instant ticks for cache
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hits, and `totalBytes` is known up front from the index — enough for a
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determinate progress bar.
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+
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Notes:
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- Meta/comment lines are skipped
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- Line strings have no trailing whitespace
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- Pass `undefined` for `end` to read to the end of the contig
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- A `refName` that is not in the index yields no lines and no error, so a
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`chr1`/`1` naming mismatch looks like an empty region. Check against
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[`getReferenceSequenceNames`](#getreferencesequencenamesopts-promisestring) if
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a query comes back unexpectedly empty
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- `start > end` throws a `TypeError`; `start === end` returns without reading
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### Without NPM (CDN)
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@@ -81,7 +94,9 @@ Notes:
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<script src="https://unpkg.com/@gmod/tabix/dist/tabix-bundle.js"></script>
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```
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See [example/index.html](example/index.html) for a working demo.
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See [example/index.html](example/index.html) for a working demo. It fetches the
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VCF over HTTP, so serve the directory (e.g. `npx serve example`) rather than
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opening the file directly.
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## API
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@@ -98,27 +113,44 @@ See [example/index.html](example/index.html) for a working demo.
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| `csiPath` | `string?` | CSI index path |
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| `csiUrl` | `string?` | CSI index URL |
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| `csiFilehandle` | `GenericFilehandle?` | CSI index filehandle |
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| `chunkCacheSize` | `number?` | Chunk LRU cache
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| `chunkCacheSize` | `number?` | Chunk LRU cache budget, in _decompressed_ bytes (default 100 MiB) |
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### `getLines(refName, start, end, opts)`
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Calls
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Calls the line callback for each line overlapping `[start, end)`. `start`
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defaults to `0` and `end` to the end of the contig when `undefined`. `opts` is
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either the callback itself or an object:
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| Option | Type | Description |
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| -------------- | -------------------------------------------------------- | --------------------------------------- |
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| `lineCallback` | `(line, fileOffset, start, end) => void` | Required |
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| `signal` | `AbortSignal?` | Aborts the in-flight reads |
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| `onProgress` | `(bytesDownloaded: number, totalBytes?: number) => void` | Called as compressed blocks are fetched |
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### `getHeader(opts?): Promise<string>`
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Returns all comment/meta lines before the first data line as a string
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Returns all comment/meta lines before the first data line as a string, matching
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what `tabix -H` prints. A header row that is not commented is therefore not
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included, even when the index counted it as a line to skip — see
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`getSkippedLines`.
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### `getHeaderBuffer(opts?): Promise<Uint8Array>`
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Returns the header as raw bytes.
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### `getSkippedLines(opts?): Promise<string[]>`
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Returns the leading lines the index says to skip (`tabix -S N`), or `[]` when it
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records none. This is where a file whose header row is not commented keeps it,
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which PLINK `.ld`, bedGraph and BED deflines routinely are.
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Separate from `getHeader` because htslib treats the two differently: a line is
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not data when the index's skip count covers it **or** it starts with the meta
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character, but `tabix -H` prints only the latter.
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### `getReferenceSequenceNames(opts?): Promise<string[]>`
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Returns reference sequence names in index order.
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to these names.
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Returns reference sequence names in index order.
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### `lineCount(refName, opts?): Promise<number>`
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@@ -130,14 +162,9 @@ reference is not in the index.
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Estimates the compressed byte size of index chunks covering the given regions.
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Useful for deciding whether a request is too large before calling `getLines`.
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##
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## Contributing
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[
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Actions.
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```bash
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pnpm version patch # or minor/major
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```
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See [CONTRIBUTING.md](CONTRIBUTING.md) for development and release steps.
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## Academic Use
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package/dist/csi.js
CHANGED
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@@ -74,7 +74,7 @@ class CSI extends indexFile_ts_1.default {
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curr += 28 + 16; // skip pseudo-bin (loffset + nchunk + 2 chunks)
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}
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else {
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firstDataLine = (0, util_ts_1.
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firstDataLine = (0, util_ts_1.minVirtualOffset)(bytes, curr, 1, firstDataLine);
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curr += 8; // loffset
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const chunkCount = dataView.getInt32(curr, true);
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curr += 4 + 16 * chunkCount;
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package/dist/csi.js.map
CHANGED
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@@ -1 +1 @@
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1
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