@gmod/tabix 3.5.5 → 3.6.0
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 +13 -12
- package/dist/indexFile.d.ts +35 -2
- package/dist/indexFile.js +71 -6
- package/dist/indexFile.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.d.ts +54 -3
- package/dist/tabixIndexedFile.js +102 -83
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/util.d.ts +1 -0
- package/dist/util.js +6 -0
- package/dist/util.js.map +1 -1
- package/esm/indexFile.d.ts +35 -2
- package/esm/indexFile.js +72 -7
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +54 -3
- package/esm/tabixIndexedFile.js +103 -84
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/util.d.ts +1 -0
- package/esm/util.js +4 -0
- package/esm/util.js.map +1 -1
- package/package.json +11 -10
- package/src/indexFile.ts +77 -8
- package/src/tabixIndexedFile.ts +130 -113
- package/src/util.ts +5 -0
package/README.md
CHANGED
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@@ -102,18 +102,19 @@ opening the file directly.
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### `new TabixIndexedFile(args)`
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-
| Arg
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-
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-
| `path`
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| `url`
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-
| `filehandle`
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| `tbiPath`
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| `tbiUrl`
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| `tbiFilehandle`
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| `csiPath`
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| `csiUrl`
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-
| `csiFilehandle`
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| `chunkCacheSize`
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| Arg | Type | Description |
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| ------------------------- | -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| `path` | `string?` | Local file path |
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| `url` | `string?` | Remote URL |
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| `filehandle` | `GenericFilehandle?` | Custom filehandle (from [generic-filehandle2](https://github.com/GMOD/generic-filehandle2)) |
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| `tbiPath` | `string?` | TBI index path (defaults to `path + '.tbi'`) |
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| `tbiUrl` | `string?` | TBI index URL |
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| `tbiFilehandle` | `GenericFilehandle?` | TBI index filehandle |
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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 budget, in _decompressed_ bytes (default 1 GiB). A retention bound, not a bound on peak memory. Size it to hold several queries: below one query's working set the hit rate drops to zero while the memory is retained anyway |
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| `chunkCacheIdleTimeoutMs` | `number?` | Drop a cached chunk once nothing has read it for this long (default 3 minutes, `0` disables). The only thing that lowers the cache while nothing is happening, and what makes the budget above a peak rather than a resting level |
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### `getLines(refName, start, end, opts)`
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package/dist/indexFile.d.ts
CHANGED
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@@ -50,6 +50,13 @@ export interface IndexData {
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export default abstract class IndexFile {
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filehandle: GenericFilehandle;
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private parseP?;
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/**
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* The signal `parseP` was started under, while it is still in flight. The
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* index is parsed once and shared by every query against the file, so without
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* this the first query to arrive would own a read all the others depend on —
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* see {@link parse}.
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*/
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private parseSignal?;
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constructor({ filehandle }: {
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filehandle: GenericFilehandle;
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});
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@@ -111,8 +118,34 @@ export default abstract class IndexFile {
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* @internal
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*/
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blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
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/**
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/**
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* Parse the index, or join the parse already running.
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*
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* The index is downloaded and parsed once for the life of this object, so it
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* is the one read here that is shared between queries — and therefore the one
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* place a cancellation can leak from the query that asked for it to a query
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* that did not. `_parse` hands `opts` straight to `readIndexBytes`, so
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* without this the first query to arrive owns a read every other query
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* depends on: when it pans away, every concurrent query fails with its abort.
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*
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* A caller that joined someone else's parse and saw it fail because *they*
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* aborted starts over rather than inheriting the failure — once, then
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* propagates. Bounding it at one attempt is what jbrowse's
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* `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
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* down, and for the reason it gives: the pathological case becomes one
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* duplicate parse rather than a recursion whose depth depends on how the
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* aborts interleave.
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*
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* A retry rather than the reference count `ChunkCache` uses, because the
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* index is parsed once for the life of the object: there is no repeated waste
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* to recover, and this is a dozen lines against restructuring the memo.
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* `@gmod/bam`'s `IndexFile` and `@gmod/cram`'s `CraiIndex` make the same
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* split for the same reason.
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*
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* @internal
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*/
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parse(opts?: Options, retried?: boolean): Promise<IndexData>;
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private startParse;
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/** @internal */
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hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
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}
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package/dist/indexFile.js
CHANGED
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@@ -5,6 +5,13 @@ const util_ts_1 = require("./util.js");
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class IndexFile {
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filehandle;
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parseP;
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/**
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* The signal `parseP` was started under, while it is still in flight. The
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* index is parsed once and shared by every query against the file, so without
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* this the first query to arrive would own a read all the others depend on —
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* see {@link parse}.
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*/
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parseSignal;
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constructor({ filehandle }) {
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this.filehandle = filehandle;
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}
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@@ -68,13 +75,71 @@ class IndexFile {
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}
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return (0, util_ts_1.optimizeChunks)(chunks, this.lowestOffset(ba, min, indexData));
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}
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// SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same owner-signal
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// tracking and one-attempt retry, and the same reasoning below.
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/**
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* Parse the index, or join the parse already running.
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*
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* The index is downloaded and parsed once for the life of this object, so it
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* is the one read here that is shared between queries — and therefore the one
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* place a cancellation can leak from the query that asked for it to a query
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* that did not. `_parse` hands `opts` straight to `readIndexBytes`, so
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* without this the first query to arrive owns a read every other query
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* depends on: when it pans away, every concurrent query fails with its abort.
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*
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* A caller that joined someone else's parse and saw it fail because *they*
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* aborted starts over rather than inheriting the failure — once, then
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* propagates. Bounding it at one attempt is what jbrowse's
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* `RemoteFileWithRangeCache.joinChunk` does with the same retry one layer
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* down, and for the reason it gives: the pathological case becomes one
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* duplicate parse rather than a recursion whose depth depends on how the
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* aborts interleave.
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*
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* A retry rather than the reference count `ChunkCache` uses, because the
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* index is parsed once for the life of the object: there is no repeated waste
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* to recover, and this is a dozen lines against restructuring the memo.
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* `@gmod/bam`'s `IndexFile` and `@gmod/cram`'s `CraiIndex` make the same
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* split for the same reason.
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*
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* @internal
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*/
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async parse(opts = {}, retried = false) {
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(0, util_ts_1.throwIfAborted)(opts.signal);
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const pending = this.parseP;
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if (!pending) {
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return this.startParse(opts);
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}
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// read before awaiting: the owner is forgotten as soon as the parse settles
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const ownerSignal = this.parseSignal;
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try {
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return await pending;
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}
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catch (e) {
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if (retried || !ownerSignal?.aborted || opts.signal?.aborted) {
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throw e;
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}
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return this.parse(opts, true);
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}
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}
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startParse(opts) {
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const pending = this._parse(opts);
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this.parseP = pending;
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this.parseSignal = opts.signal;
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// Drop a rejection rather than keeping it, so one transient failure does not
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// poison the index for the lifetime of the file. Both branches are
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// identity-checked so a retry started after this settles is not cleared by
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// the attempt it already replaced.
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pending.then(() => {
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if (this.parseP === pending) {
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this.parseSignal = undefined;
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}
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}, () => {
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if (this.parseP === pending) {
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this.parseP = undefined;
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this.parseSignal = undefined;
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}
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});
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return
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return pending;
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}
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/** @internal */
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async hasRefSeq(seqId, opts = {}) {
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package/dist/indexFile.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAAA,2DAA6C;AAE7C,
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