@gmod/tabix 3.4.3 → 3.5.1
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 +31 -20
- package/dist/csi.d.ts +8 -0
- package/dist/csi.js +29 -3
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +2 -0
- package/dist/indexFile.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.js +43 -5
- package/dist/tabixIndexedFile.js.map +1 -1
- package/esm/csi.d.ts +8 -0
- package/esm/csi.js +29 -3
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +2 -0
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.js +43 -5
- package/esm/tabixIndexedFile.js.map +1 -1
- package/package.json +15 -14
- package/src/csi.ts +33 -3
- package/src/indexFile.ts +2 -0
- package/src/tabixIndexedFile.ts +46 -9
package/README.md
CHANGED
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@@ -42,14 +42,16 @@ const file = new TabixIndexedFile({
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### getLines
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-
Fetches lines overlapping a region. `start`/`end` are 0-based half-open
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Fetches lines overlapping a region. `start`/`end` are 0-based half-open
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coordinates (unlike the tabix CLI which uses 1-based closed).
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```typescript
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const lines: string[] = []
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await file.getLines('chr1', 200, 300, line => lines.push(line))
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```
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The callback also receives the virtual file offset and parsed coordinates for
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The callback also receives the virtual file offset and parsed coordinates for
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the line:
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```typescript
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await file.getLines('chr1', 200, 300, (line, fileOffset, start, end) => {
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@@ -68,6 +70,7 @@ await file.getLines('chr1', 200, 300, {
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```
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Notes:
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+
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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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@@ -84,24 +87,25 @@ See [example/index.html](example/index.html) for a working demo.
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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` | `number?`
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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 size in bytes (default 5 MiB) |
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### `getLines(refName, start, end, opts)`
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Calls `opts` (or `opts.lineCallback`) for each line overlapping `[start, end)`.
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Callback signature:
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Callback signature:
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`(line: string, fileOffset: number, start: number, end: number) => void`
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### `getHeader(opts?): Promise<string>`
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@@ -113,19 +117,23 @@ Returns the header as raw bytes.
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### `getReferenceSequenceNames(opts?): Promise<string[]>`
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Returns reference sequence names in index order. `renameRefSeqs` is not applied
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Returns reference sequence names in index order. `renameRefSeqs` is not applied
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to these names.
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### `lineCount(refName, opts?): Promise<number>`
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Returns the number of data lines on the given reference, or `-1` if the
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Returns the number of data lines on the given reference, or `-1` if the
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reference is not in the index.
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### `bytesForRegions(regions, opts?): Promise<number>`
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Estimates the compressed byte size of index chunks covering the given regions.
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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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## Publishing
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[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
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[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
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Actions.
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```bash
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pnpm version patch # or minor/major
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@@ -133,7 +141,10 @@ pnpm version patch # or minor/major
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## Academic Use
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-
This package was written with funding from the [NHGRI](http://genome.gov) as
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This package was written with funding from the [NHGRI](http://genome.gov) as
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part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
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project that you publish, please cite the most recent JBrowse paper, which will
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be linked from [jbrowse.org](http://jbrowse.org).
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## License
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package/dist/csi.d.ts
CHANGED
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@@ -50,6 +50,14 @@ export default class CSI extends IndexFile {
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format: string;
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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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* CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
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* indexed bin covering `beg` is the earliest virtual offset any record
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* overlapping `beg` can have, so chunks ending at or before it are dead.
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* Walks leaf -> previous sibling -> parent until an indexed bin is found.
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* SYNC: htslib hts_itr_query min_off computation
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*/
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private minOffset;
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/** @internal */
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reg2bins(beg: number, end: number): (readonly [number, number])[];
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}
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package/dist/csi.js
CHANGED
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@@ -90,6 +90,7 @@ class CSI extends indexFile_ts_1.default {
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const binCount = dataView.getInt32(pos, true);
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pos += 4;
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const binIndex = {};
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const loffsets = {};
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let stats;
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for (let j = 0; j < binCount; j++) {
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const bin = dataView.getUint32(pos, true);
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pos += 28 + 16;
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}
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else {
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loffsets[bin] = (0, virtualOffset_ts_1.fromBytes)(bytes, pos);
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pos += 8;
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const chunkCount = dataView.getInt32(pos, true);
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pos += 4;
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const chunks = Array.from({ length: chunkCount });
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@@ -111,7 +113,7 @@ class CSI extends indexFile_ts_1.default {
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}
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}
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(0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat());
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return { binIndex, stats };
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return { binIndex, loffsets, stats };
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}
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return {
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...aux,
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}
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}
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}
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return (0, util_ts_1.optimizeChunks)(chunks);
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return (0, util_ts_1.optimizeChunks)(chunks, this.minOffset(ba.loffsets, min));
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}
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/**
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* CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
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* indexed bin covering `beg` is the earliest virtual offset any record
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* overlapping `beg` can have, so chunks ending at or before it are dead.
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* Walks leaf -> previous sibling -> parent until an indexed bin is found.
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* SYNC: htslib hts_itr_query min_off computation
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*/
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minOffset(loffsets, beg) {
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let found;
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if (loffsets) {
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// first bin of the deepest level, i.e. (8**depth - 1) / 7
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let bin = (lshift(1, 3 * this.depth) - 1) / 7 + rshift(beg, this.minShift);
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while (found === undefined && bin > 0) {
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found = loffsets[bin];
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if (found === undefined) {
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const parent = Math.floor((bin - 1) / 8);
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const firstChild = parent * 8 + 1;
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bin = bin > firstChild ? bin - 1 : parent;
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}
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}
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found ??= loffsets[0];
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}
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return found;
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}
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/** @internal */
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reg2bins(beg, end) {
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package/dist/csi.js.map
CHANGED
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@@ -1 +1 @@
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+
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|
package/dist/indexFile.d.ts
CHANGED
|
@@ -16,6 +16,8 @@ export interface RefIndex {
|
|
|
16
16
|
lineCount: number;
|
|
17
17
|
};
|
|
18
18
|
linearIndex?: VirtualOffset[];
|
|
19
|
+
/** CSI only: per-bin loffset, the linear index's equivalent for pruning */
|
|
20
|
+
loffsets?: Record<number, VirtualOffset>;
|
|
19
21
|
}
|
|
20
22
|
export interface IndexData {
|
|
21
23
|
refNameToId: Record<string, number>;
|
package/dist/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAyCA,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"}
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