@gmod/tabix 3.5.7 → 3.6.0

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Files changed (24) hide show
  1. package/README.md +13 -12
  2. package/dist/indexFile.d.ts +5 -5
  3. package/dist/indexFile.js +16 -23
  4. package/dist/indexFile.js.map +1 -1
  5. package/dist/tabix-bundle.js +1 -1
  6. package/dist/tabixIndexedFile.d.ts +54 -3
  7. package/dist/tabixIndexedFile.js +102 -83
  8. package/dist/tabixIndexedFile.js.map +1 -1
  9. package/dist/util.d.ts +1 -18
  10. package/dist/util.js +6 -31
  11. package/dist/util.js.map +1 -1
  12. package/esm/indexFile.d.ts +5 -5
  13. package/esm/indexFile.js +16 -23
  14. package/esm/indexFile.js.map +1 -1
  15. package/esm/tabixIndexedFile.d.ts +54 -3
  16. package/esm/tabixIndexedFile.js +103 -84
  17. package/esm/tabixIndexedFile.js.map +1 -1
  18. package/esm/util.d.ts +1 -18
  19. package/esm/util.js +4 -30
  20. package/esm/util.js.map +1 -1
  21. package/package.json +11 -9
  22. package/src/indexFile.ts +21 -24
  23. package/src/tabixIndexedFile.ts +130 -113
  24. package/src/util.ts +4 -30
package/README.md CHANGED
@@ -102,18 +102,19 @@ opening the file directly.
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  ### `new TabixIndexedFile(args)`
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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 100 MiB) |
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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
@@ -136,11 +136,11 @@ export default abstract class IndexFile {
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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` gets from
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- * `@gmod/abortable-promise-cache`, because the index is parsed once for the
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- * life of the object: there is no repeated waste to recover, and this is a
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- * dozen lines against restructuring the memo. `@gmod/bam`'s `IndexFile` and
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- * `@gmod/cram`'s `CraiIndex` make the same split for the same reason.
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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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  */
package/dist/indexFile.js CHANGED
@@ -75,6 +75,8 @@ 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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  *
@@ -93,11 +95,11 @@ class IndexFile {
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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` gets from
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- * `@gmod/abortable-promise-cache`, because the index is parsed once for the
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- * life of the object: there is no repeated waste to recover, and this is a
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- * dozen lines against restructuring the memo. `@gmod/bam`'s `IndexFile` and
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- * `@gmod/cram`'s `CraiIndex` make the same split for the same reason.
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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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  */
@@ -124,28 +126,19 @@ class IndexFile {
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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. Identity-checked so a retry
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- // started after this settles is not cleared by the attempt it replaced.
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- //
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- // Written as one try/catch rather than `.then(onFulfilled, onRejected)`
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- // because `unicorn/prefer-then-catch` rewrites the two-argument form to
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- // `.then(...).catch(...)`, which is not the same thing — that catch would
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- // also swallow anything the fulfilment handler threw.
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- void (async () => {
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- let failed = false;
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- try {
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- await pending;
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- }
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- catch {
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- failed = true;
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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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- if (failed) {
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- this.parseP = undefined;
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- }
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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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+ });
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  return pending;
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  }
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  /** @internal */
package/dist/indexFile.js.map CHANGED
@@ -1 +1 @@
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