@gmod/tabix 3.4.0 → 3.4.2
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/dist/chunk.d.ts +2 -1
- package/dist/chunk.js +8 -2
- package/dist/chunk.js.map +1 -1
- package/dist/csi.js +5 -1
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +6 -0
- package/dist/indexFile.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.d.ts +1 -1
- package/dist/tbi.js +5 -1
- package/dist/tbi.js.map +1 -1
- package/dist/util.d.ts +1 -0
- package/dist/util.js +34 -1
- package/dist/util.js.map +1 -1
- package/esm/chunk.d.ts +2 -1
- package/esm/chunk.js +8 -2
- package/esm/chunk.js.map +1 -1
- package/esm/csi.js +6 -2
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +6 -0
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +1 -1
- package/esm/tbi.js +6 -2
- package/esm/tbi.js.map +1 -1
- package/esm/util.d.ts +1 -0
- package/esm/util.js +33 -1
- package/esm/util.js.map +1 -1
- package/package.json +8 -8
- package/src/chunk.ts +13 -2
- package/src/csi.ts +6 -1
- package/src/indexFile.ts +6 -0
- package/src/tabixIndexedFile.ts +1 -1
- package/src/tbi.ts +9 -1
- package/src/util.ts +34 -0
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@@ -12,7 +12,7 @@ interface GetLinesOpts {
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* which is the natural unit since chunk byte sizes are known up front from
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* the index. Lets callers render a determinate download progress bar.
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*/
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-
onProgress?: (bytesDownloaded: number, totalBytes
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+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
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}
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/**
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* Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
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package/dist/tbi.js
CHANGED
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@@ -28,7 +28,10 @@ function reg2bins(beg, end) {
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class TabixIndex extends indexFile_ts_1.default {
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/** @internal */
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async _parse(opts = {}) {
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-
const buf = await this.filehandle.readFile({
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+
const buf = await this.filehandle.readFile({
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signal: opts.signal,
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onProgress: opts.onProgress,
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});
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const bytes = (await (0, bgzf_filehandle_1.unzip)(buf));
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const dataView = new DataView(bytes.buffer);
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if (dataView.getUint32(0, true) !== TBI_MAGIC) {
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@@ -118,6 +121,7 @@ class TabixIndex extends indexFile_ts_1.default {
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linearIndex[k] = (0, virtualOffset_ts_1.fromBytes)(bytes, pos);
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pos += 8;
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}
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+
(0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
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return { binIndex, linearIndex, stats };
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}
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return {
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package/dist/tbi.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAsC;AACtC,
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1
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+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAsC;AACtC,uCAOkB;AAClB,yDAA8C;AAK9C,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAErC;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAS;IAC/C,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAA;QACF,MAAM,KAAK,GAAG,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAE1C,oEAAoE;QACpE,MAAM,EACJ,WAAW,EACX,WAAW,EACX,cAAc,EACd,MAAM,EACN,aAAa,EACb,QAAQ,EACR,SAAS,GACV,GAAG,IAAA,sBAAY,EAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QAC1B,+EAA+E;QAC/E,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAErD,iEAAiE;QACjE,mEAAmE;QACnE,IAAI,IAAI,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACjC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAa,EAAE,CAAA;QAE5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAChD,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,IAAI,IAAI,EAAE,GAAG,UAAU,CAAA;gBACzB,CAAC;qBAAM,CAAC;oBACN,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;wBACpE,IAAI,IAAI,EAAE,CAAA;oBACZ,CAAC;gBACH,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;gBACpE,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YAC5B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,GAAG,GAAG,KAAK,CAAA;YACf,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAC7C,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBACzC,GAAG,IAAI,CAAC,CAAA;gBACR,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACzC,CAAC;oBACD,GAAG,IAAI,EAAE,GAAG,UAAU,CAAA;gBACxB,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAA;oBACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CACnB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,EACrB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,GAAG,CAAC,CAAC,EACzB,GAAG,CACJ,CAAA;wBACD,GAAG,IAAI,EAAE,CAAA;oBACX,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAChD,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAgB,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC,CAAA;YACtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,CAAA;gBACtC,GAAG,IAAI,CAAC,CAAA;YACV,CAAC;YACD,IAAA,wBAAc,EACZ,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,EAC9B,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CACtC,CAAA;YACD,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;QACzC,CAAC;QAED,OAAO;YACL,OAAO,EAAE,IAAA,wBAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;YACR,YAAY;YACZ,YAAY;YACZ,SAAS;YACT,aAAa;YACb,aAAa;YACb,cAAc;YACd,MAAM;YACN,WAAW;YACX,WAAW;YACX,YAAY,EAAE,CAAC,IAAI,EAAE;SACtB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,GAAW,EACX,GAAW,EACX,OAAgB,EAAE;QAElB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,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,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,WAAW,GAAG,EAAE,CAAC,WAAW,IAAI,EAAE,CAAA;QACxC,sEAAsE;QACtE,yCAAyC;QACzC,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YAC7C,OAAO,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAA;QAC1D,CAAC;QAED,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA,CAAC,uCAAuC;QAClF,MAAM,MAAM,GAAY,EAAE,CAAA;QAE1B,sEAAsE;QACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAClC,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;wBAC1B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBAChB,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,2EAA2E;QAC3E,sEAAsE;QACtE,oDAAoD;QACpD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAEvE,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF;AA1LD,6BA0LC"}
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package/dist/util.d.ts
CHANGED
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@@ -1,6 +1,7 @@
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1
1
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import Chunk from './chunk.ts';
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2
2
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import type VirtualOffset from './virtualOffset.ts';
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3
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export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
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+
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
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export declare function findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
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export declare function parseNameBytes(namesBytes: Uint8Array): {
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refNameToId: Record<string, number>;
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package/dist/util.js
CHANGED
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@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.optimizeChunks = optimizeChunks;
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exports.clampChunkEnds = clampChunkEnds;
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exports.findFirstData = findFirstData;
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exports.parseNameBytes = parseNameBytes;
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exports.parseAuxData = parseAuxData;
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@@ -61,7 +62,7 @@ function optimizeChunks(chunks, lowest) {
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const cmp = chunkMaxBlock - lastMaxBlock ||
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chunk.maxv.dataPosition - lastChunk.maxv.dataPosition;
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if (cmp > 0) {
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-
mergedChunks[mergedChunks.length - 1] = new chunk_ts_1.default(lastChunk.minv, chunk.maxv, lastChunk.bin);
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mergedChunks[mergedChunks.length - 1] = new chunk_ts_1.default(lastChunk.minv, chunk.maxv, lastChunk.bin, chunk.endPosition);
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lastMaxBlock = chunkMaxBlock;
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}
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}
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return mergedChunks;
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}
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// Tighten each chunk's endPosition (default: a full max-size BGZF block past
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// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
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// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
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// since blocks don't overlap, the first boundary strictly greater than a chunk's
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// maxv.blockPosition is an upper bound on where that final block ends — always at
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// least the true block end, so the clamped fetch still contains the whole block.
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// Shrinks both the byte estimate and the actual fetch with no extra I/O.
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+
function clampChunkEnds(chunks, extraBoundaries = []) {
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+
const boundaries = [...extraBoundaries];
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for (const c of chunks) {
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boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
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}
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+
boundaries.sort((a, b) => a - b);
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for (const c of chunks) {
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const max = c.maxv.blockPosition;
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// first boundary strictly greater than max
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let lo = 0;
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let hi = boundaries.length;
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while (lo < hi) {
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const mid = (lo + hi) >>> 1;
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if (boundaries[mid] > max) {
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hi = mid;
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}
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else {
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lo = mid + 1;
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}
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}
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if (lo < boundaries.length) {
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c.endPosition = Math.min(c.endPosition, boundaries[lo]);
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}
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}
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}
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function findFirstData(currentFdl, virtualOffset) {
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return !currentFdl || currentFdl.compareTo(virtualOffset) > 0
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? virtualOffset
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package/dist/util.js.map
CHANGED
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AAQA,
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|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AAQA,wCAuEC;AASD,wCAwBC;AAED,sCAOC;AAED,wCAoBC;AAQD,oCA8BC;AAED,wCAEC;AAGD,wCAgBC;AA5MD,mEAAoC;AAEpC,0DAA8B;AAC9B,uCAAmD;AAInD,qDAAqD;AACrD,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,uEAAuE;IACvE,wEAAwE;IACxE,2EAA2E;IAC3E,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,GAAG,GACP,KAAK,CAAC,IAAI,CAAC,aAAa,GAAG,WAAW;gBACtC,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACtC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,4EAA4E;IAC5E,0DAA0D;IAC1D,oEAAoE;IACpE,MAAM,YAAY,GAAY,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAClD,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAElD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,IACE,aAAa,GAAG,YAAY,GAAG,MAAM;YACrC,aAAa,GAAG,YAAY,GAAG,SAAS,EACxC,CAAC;YACD,MAAM,SAAS,GAAG,YAAY,CAAC,EAAE,CAAC,CAAC,CAAC,CAAE,CAAA;YACtC,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,YAAY,CAAA;YACvD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,kBAAK,CAC/C,SAAS,CAAC,IAAI,EACd,KAAK,CAAC,IAAI,EACV,SAAS,CAAC,GAAG,EACb,KAAK,CAAC,WAAW,CAClB,CAAA;gBACD,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,6EAA6E;AAC7E,kFAAkF;AAClF,kFAAkF;AAClF,iFAAiF;AACjF,kFAAkF;AAClF,iFAAiF;AACjF,yEAAyE;AACzE,SAAgB,cAAc,CAAC,MAAe,EAAE,kBAA4B,EAAE;IAC5E,MAAM,UAAU,GAAG,CAAC,GAAG,eAAe,CAAC,CAAA;IACvC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;IAC7D,CAAC;IACD,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAEhC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,aAAa,CAAA;QAChC,2CAA2C;QAC3C,IAAI,EAAE,GAAG,CAAC,CAAA;QACV,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QAC1B,OAAO,EAAE,GAAG,EAAE,EAAE,CAAC;YACf,MAAM,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;YAC3B,IAAI,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,EAAE,CAAC;gBAC3B,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,EAAE,GAAG,GAAG,GAAG,CAAC,CAAA;YACd,CAAC;QACH,CAAC;QACD,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;YAC3B,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,UAAU,CAAC,EAAE,CAAE,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAgB,aAAa,CAC3B,UAAqC,EACrC,aAA4B;IAE5B,OAAO,CAAC,UAAU,IAAI,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;QAC3D,CAAC,CAAC,aAAa;QACf,CAAC,CAAC,UAAU,CAAA;AAChB,CAAC;AAED,SAAgB,cAAc,CAAC,UAAsB;IACnD,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,OAAO,CAAC,CAAA;IACxC,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;QAC/B,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QACtC,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE,CAAC;YACf,MAAK;QACP,CAAC;QACD,IAAI,GAAG,GAAG,GAAG,EAAE,CAAC;YACd,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;YAC7D,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;YAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;QAClC,CAAC;QACD,GAAG,GAAG,GAAG,GAAG,CAAC,CAAA;QACb,SAAS,EAAE,CAAA;IACb,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,YAAY,GAA2B;IAC3C,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAgB,YAAY,CAAC,KAAiB,EAAE,MAAc;IAC5D,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IACnD,MAAM,cAAc,GAClB,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;IACrE,MAAM,MAAM,GAAG,YAAY,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;IAC9C,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;IACrE,CAAC;IACD,MAAM,aAAa,GAAG;QACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;KAC1C,CAAA;IACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,cAAc,CACjD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;IACD,OAAO;QACL,WAAW;QACX,WAAW;QACX,SAAS;QACT,QAAQ;QACR,aAAa;QACb,MAAM;QACN,cAAc;KACf,CAAA;AACH,CAAC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO,EAAE,SAAS,EAAE,IAAA,iCAAuB,EAAC,KAAK,EAAE,MAAM,CAAC,EAAE,CAAA;AAC9D,CAAC;AAED,0DAA0D;AAC1D,SAAgB,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,GAAG,GAAG,IAAI,mBAAG,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAC3C,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,MAAM,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC7B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QACxB,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC"}
|
package/esm/chunk.d.ts
CHANGED
|
@@ -3,7 +3,8 @@ export default class Chunk {
|
|
|
3
3
|
minv: VirtualOffset;
|
|
4
4
|
maxv: VirtualOffset;
|
|
5
5
|
bin: number;
|
|
6
|
-
|
|
6
|
+
endPosition: number;
|
|
7
|
+
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, endPosition?: number);
|
|
7
8
|
toString(): string;
|
|
8
9
|
fetchedSize(): number;
|
|
9
10
|
}
|
package/esm/chunk.js
CHANGED
|
@@ -3,16 +3,22 @@ export default class Chunk {
|
|
|
3
3
|
minv;
|
|
4
4
|
maxv;
|
|
5
5
|
bin;
|
|
6
|
-
|
|
6
|
+
// Absolute byte offset where the fetch for this chunk ends. The compressed
|
|
7
|
+
// size of the final BGZF block (the one at maxv.blockPosition) is unknown
|
|
8
|
+
// from the index, so this defaults to a full max-size block past maxv. It can
|
|
9
|
+
// be tightened to the next known block boundary via clampChunkEnds.
|
|
10
|
+
endPosition;
|
|
11
|
+
constructor(minv, maxv, bin, endPosition = maxv.blockPosition + (1 << 16)) {
|
|
7
12
|
this.minv = minv;
|
|
8
13
|
this.maxv = maxv;
|
|
9
14
|
this.bin = bin;
|
|
15
|
+
this.endPosition = endPosition;
|
|
10
16
|
}
|
|
11
17
|
toString() {
|
|
12
18
|
return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
|
|
13
19
|
}
|
|
14
20
|
fetchedSize() {
|
|
15
|
-
return this.
|
|
21
|
+
return this.endPosition - this.minv.blockPosition;
|
|
16
22
|
}
|
|
17
23
|
}
|
|
18
24
|
//# sourceMappingURL=chunk.js.map
|
package/esm/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IACjB,IAAI,CAAe;IACnB,IAAI,CAAe;IACnB,GAAG,CAAQ;
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IACjB,IAAI,CAAe;IACnB,IAAI,CAAe;IACnB,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACnD,CAAC;CACF"}
|
package/esm/csi.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
2
|
import Chunk from "./chunk.js";
|
|
3
3
|
import IndexFile from "./indexFile.js";
|
|
4
|
-
import { findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
|
|
4
|
+
import { clampChunkEnds, findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
|
|
5
5
|
import { fromBytes } from "./virtualOffset.js";
|
|
6
6
|
const CSI1_MAGIC = 21_582_659; // CSI\1
|
|
7
7
|
const CSI2_MAGIC = 38_359_875; // CSI\2
|
|
@@ -29,7 +29,10 @@ export default class CSI extends IndexFile {
|
|
|
29
29
|
}
|
|
30
30
|
/** @internal */
|
|
31
31
|
async _parse(opts = {}) {
|
|
32
|
-
const buf = await this.filehandle.readFile({
|
|
32
|
+
const buf = await this.filehandle.readFile({
|
|
33
|
+
signal: opts.signal,
|
|
34
|
+
onProgress: opts.onProgress,
|
|
35
|
+
});
|
|
33
36
|
const bytes = (await unzip(buf));
|
|
34
37
|
const dataView = new DataView(bytes.buffer);
|
|
35
38
|
const magic = dataView.getUint32(0, true);
|
|
@@ -112,6 +115,7 @@ export default class CSI extends IndexFile {
|
|
|
112
115
|
binIndex[bin] = chunks;
|
|
113
116
|
}
|
|
114
117
|
}
|
|
118
|
+
clampChunkEnds(Object.values(binIndex).flat());
|
|
115
119
|
return { binIndex, stats };
|
|
116
120
|
}
|
|
117
121
|
return {
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,aAAa,EACb,cAAc,EACd,cAAc,EACd,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAM9C,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AACtC,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AAEtC,gFAAgF;AAChF,wDAAwD;AACxD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAChC,YAAY,CAAQ;IACpB,KAAK,CAAQ;IACb,QAAQ,CAAQ;IACxB,YAAY,IAAuC;QACjD,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,gBAAgB;IAChB,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,cAAc,EACd,aAAa,EACb,cAAc,EACd,cAAc,EACd,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAM9C,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AACtC,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AAEtC,gFAAgF;AAChF,wDAAwD;AACxD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAChC,YAAY,CAAQ;IACpB,KAAK,CAAQ;IACb,QAAQ,CAAQ;IACxB,YAAY,IAAuC;QACjD,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,gBAAgB;IAChB,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAA;QACF,MAAM,KAAK,GAAG,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,UAAU,CAAA;QACd,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,yBAAyB,KAAK,GAAG,CAAC,CAAA;QACpD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GACP,SAAS,IAAI,EAAE;YACb,CAAC,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;YACzB,CAAC,CAAC;gBACE,WAAW,EAAE,EAAc;gBAC3B,WAAW,EAAE,EAA4B;gBACzC,QAAQ,EAAE,SAAS;gBACnB,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;gBAC3C,cAAc,EAAE,sBAAsB;gBACtC,MAAM,EAAE,SAAS;aAClB,CAAA;QACP,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,iEAAiE;QACjE,gFAAgF;QAChF,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAa,EAAE,CAAA;QAE5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA,CAAC,gDAAgD;gBAClE,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA,CAAC,UAAU;oBACpB,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YAC5B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,GAAG,GAAG,KAAK,CAAA;YACf,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAC7C,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBACzC,GAAG,IAAI,CAAC,CAAA;gBACR,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACvC,GAAG,IAAI,EAAE,GAAG,EAAE,CAAA;gBAChB,CAAC;qBAAM,CAAC;oBACN,GAAG,IAAI,CAAC,CAAA,CAAC,uCAAuC;oBAChD,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAA;oBACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CACnB,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,EACrB,SAAS,CAAC,KAAK,EAAE,GAAG,GAAG,CAAC,CAAC,EACzB,GAAG,CACJ,CAAA;wBACD,GAAG,IAAI,EAAE,CAAA;oBACX,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,cAAc,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QAC5B,CAAC;QAED,OAAO;YACL,GAAG,GAAG;YACN,GAAG,EAAE,IAAI;YACT,QAAQ;YACR,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,aAAa;YACb,UAAU;YACV,OAAO,EAAE,cAAc,CAAC,UAAU,CAAC;YACnC,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,YAAY;YACZ,YAAY;SACb,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,GAAW,EACX,GAAW,EACX,OAAgB,EAAE;QAElB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,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,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QAED,uCAAuC;QACvC,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAY,EAAE,CAAA;QAE1B,sEAAsE;QACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAClC,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;wBAC1B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBAChB,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,cAAc,CAAC,MAAM,CAAC,CAAA;IAC/B,CAAC;IAED,gBAAgB;IAChB,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,MAAM,MAAM,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QACpD,IAAI,GAAG,GAAG,MAAM,EAAE,CAAC;YACjB,GAAG,GAAG,MAAM,CAAA;QACd,CAAC;QACD,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
|
package/esm/indexFile.d.ts
CHANGED
|
@@ -3,6 +3,12 @@ import type VirtualOffset from './virtualOffset.ts';
|
|
|
3
3
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
4
|
export interface Options {
|
|
5
5
|
signal?: AbortSignal;
|
|
6
|
+
/**
|
|
7
|
+
* Called as the index (.tbi/.csi) is downloaded, with cumulative downloaded
|
|
8
|
+
* bytes and the total. The index is a whole-file read, so this streams real
|
|
9
|
+
* byte progress. Lets callers show a determinate "downloading index" bar.
|
|
10
|
+
*/
|
|
11
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
6
12
|
}
|
|
7
13
|
export interface RefIndex {
|
|
8
14
|
binIndex: Record<number, Chunk[]>;
|
package/esm/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":"AAuCA,MAAM,CAAC,OAAO,OAAgB,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"}
|
|
@@ -12,7 +12,7 @@ interface GetLinesOpts {
|
|
|
12
12
|
* which is the natural unit since chunk byte sizes are known up front from
|
|
13
13
|
* the index. Lets callers render a determinate download progress bar.
|
|
14
14
|
*/
|
|
15
|
-
onProgress?: (bytesDownloaded: number, totalBytes
|
|
15
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
16
16
|
}
|
|
17
17
|
/**
|
|
18
18
|
* Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
|
package/esm/tbi.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
2
|
import Chunk from "./chunk.js";
|
|
3
3
|
import IndexFile from "./indexFile.js";
|
|
4
|
-
import { findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
|
|
4
|
+
import { clampChunkEnds, findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
|
|
5
5
|
import { fromBytes } from "./virtualOffset.js";
|
|
6
6
|
const TBI_MAGIC = 21_578_324; // TBI\1
|
|
7
7
|
/**
|
|
@@ -23,7 +23,10 @@ function reg2bins(beg, end) {
|
|
|
23
23
|
export default class TabixIndex extends IndexFile {
|
|
24
24
|
/** @internal */
|
|
25
25
|
async _parse(opts = {}) {
|
|
26
|
-
const buf = await this.filehandle.readFile({
|
|
26
|
+
const buf = await this.filehandle.readFile({
|
|
27
|
+
signal: opts.signal,
|
|
28
|
+
onProgress: opts.onProgress,
|
|
29
|
+
});
|
|
27
30
|
const bytes = (await unzip(buf));
|
|
28
31
|
const dataView = new DataView(bytes.buffer);
|
|
29
32
|
if (dataView.getUint32(0, true) !== TBI_MAGIC) {
|
|
@@ -113,6 +116,7 @@ export default class TabixIndex extends IndexFile {
|
|
|
113
116
|
linearIndex[k] = fromBytes(bytes, pos);
|
|
114
117
|
pos += 8;
|
|
115
118
|
}
|
|
119
|
+
clampChunkEnds(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
|
|
116
120
|
return { binIndex, linearIndex, stats };
|
|
117
121
|
}
|
|
118
122
|
return {
|
package/esm/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,aAAa,EACb,cAAc,EACd,cAAc,EACd,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAK9C,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAErC;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;IAC/C,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,
|
|
1
|
+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,cAAc,EACd,aAAa,EACb,cAAc,EACd,cAAc,EACd,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAK9C,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAErC;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;IAC/C,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAA;QACF,MAAM,KAAK,GAAG,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAE1C,oEAAoE;QACpE,MAAM,EACJ,WAAW,EACX,WAAW,EACX,cAAc,EACd,MAAM,EACN,aAAa,EACb,QAAQ,EACR,SAAS,GACV,GAAG,YAAY,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QAC1B,+EAA+E;QAC/E,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAErD,iEAAiE;QACjE,mEAAmE;QACnE,IAAI,IAAI,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACjC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAa,EAAE,CAAA;QAE5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAChD,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,IAAI,IAAI,EAAE,GAAG,UAAU,CAAA;gBACzB,CAAC;qBAAM,CAAC;oBACN,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;wBACpE,IAAI,IAAI,EAAE,CAAA;oBACZ,CAAC;gBACH,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;gBACpE,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YAC5B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,GAAG,GAAG,KAAK,CAAA;YACf,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAC7C,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBACzC,GAAG,IAAI,CAAC,CAAA;gBACR,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACzC,CAAC;oBACD,GAAG,IAAI,EAAE,GAAG,UAAU,CAAA;gBACxB,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAA;oBACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CACnB,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,EACrB,SAAS,CAAC,KAAK,EAAE,GAAG,GAAG,CAAC,CAAC,EACzB,GAAG,CACJ,CAAA;wBACD,GAAG,IAAI,EAAE,CAAA;oBACX,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAChD,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAgB,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC,CAAA;YACtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,WAAW,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;gBACtC,GAAG,IAAI,CAAC,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|
package/esm/util.d.ts
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
2
|
import type VirtualOffset from './virtualOffset.ts';
|
|
3
3
|
export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
|
|
4
|
+
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
|
|
4
5
|
export declare function findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
|
|
5
6
|
export declare function parseNameBytes(namesBytes: Uint8Array): {
|
|
6
7
|
refNameToId: Record<string, number>;
|
package/esm/util.js
CHANGED
|
@@ -50,7 +50,7 @@ export function optimizeChunks(chunks, lowest) {
|
|
|
50
50
|
const cmp = chunkMaxBlock - lastMaxBlock ||
|
|
51
51
|
chunk.maxv.dataPosition - lastChunk.maxv.dataPosition;
|
|
52
52
|
if (cmp > 0) {
|
|
53
|
-
mergedChunks[mergedChunks.length - 1] = new Chunk(lastChunk.minv, chunk.maxv, lastChunk.bin);
|
|
53
|
+
mergedChunks[mergedChunks.length - 1] = new Chunk(lastChunk.minv, chunk.maxv, lastChunk.bin, chunk.endPosition);
|
|
54
54
|
lastMaxBlock = chunkMaxBlock;
|
|
55
55
|
}
|
|
56
56
|
}
|
|
@@ -62,6 +62,38 @@ export function optimizeChunks(chunks, lowest) {
|
|
|
62
62
|
}
|
|
63
63
|
return mergedChunks;
|
|
64
64
|
}
|
|
65
|
+
// Tighten each chunk's endPosition (default: a full max-size BGZF block past
|
|
66
|
+
// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
|
|
67
|
+
// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
|
|
68
|
+
// since blocks don't overlap, the first boundary strictly greater than a chunk's
|
|
69
|
+
// maxv.blockPosition is an upper bound on where that final block ends — always at
|
|
70
|
+
// least the true block end, so the clamped fetch still contains the whole block.
|
|
71
|
+
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
72
|
+
export function clampChunkEnds(chunks, extraBoundaries = []) {
|
|
73
|
+
const boundaries = [...extraBoundaries];
|
|
74
|
+
for (const c of chunks) {
|
|
75
|
+
boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
|
|
76
|
+
}
|
|
77
|
+
boundaries.sort((a, b) => a - b);
|
|
78
|
+
for (const c of chunks) {
|
|
79
|
+
const max = c.maxv.blockPosition;
|
|
80
|
+
// first boundary strictly greater than max
|
|
81
|
+
let lo = 0;
|
|
82
|
+
let hi = boundaries.length;
|
|
83
|
+
while (lo < hi) {
|
|
84
|
+
const mid = (lo + hi) >>> 1;
|
|
85
|
+
if (boundaries[mid] > max) {
|
|
86
|
+
hi = mid;
|
|
87
|
+
}
|
|
88
|
+
else {
|
|
89
|
+
lo = mid + 1;
|
|
90
|
+
}
|
|
91
|
+
}
|
|
92
|
+
if (lo < boundaries.length) {
|
|
93
|
+
c.endPosition = Math.min(c.endPosition, boundaries[lo]);
|
|
94
|
+
}
|
|
95
|
+
}
|
|
96
|
+
}
|
|
65
97
|
export function findFirstData(currentFdl, virtualOffset) {
|
|
66
98
|
return !currentFdl || currentFdl.compareTo(virtualOffset) > 0
|
|
67
99
|
? virtualOffset
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,oBAAoB,CAAA;AAEpC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AAInD,qDAAqD;AACrD,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,uEAAuE;IACvE,wEAAwE;IACxE,2EAA2E;IAC3E,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,GAAG,GACP,KAAK,CAAC,IAAI,CAAC,aAAa,GAAG,WAAW;gBACtC,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACtC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,4EAA4E;IAC5E,0DAA0D;IAC1D,oEAAoE;IACpE,MAAM,YAAY,GAAY,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAClD,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAElD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,IACE,aAAa,GAAG,YAAY,GAAG,MAAM;YACrC,aAAa,GAAG,YAAY,GAAG,SAAS,EACxC,CAAC;YACD,MAAM,SAAS,GAAG,YAAY,CAAC,EAAE,CAAC,CAAC,CAAC,CAAE,CAAA;YACtC,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,YAAY,CAAA;YACvD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,KAAK,CAC/C,SAAS,CAAC,IAAI,EACd,KAAK,CAAC,IAAI,EACV,SAAS,CAAC,GAAG,EACb,KAAK,CAAC,WAAW,CAClB,CAAA;gBACD,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,6EAA6E;AAC7E,kFAAkF;AAClF,kFAAkF;AAClF,iFAAiF;AACjF,kFAAkF;AAClF,iFAAiF;AACjF,yEAAyE;AACzE,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,kBAA4B,EAAE;IAC5E,MAAM,UAAU,GAAG,CAAC,GAAG,eAAe,CAAC,CAAA;IACvC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;IAC7D,CAAC;IACD,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAEhC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,aAAa,CAAA;QAChC,2CAA2C;QAC3C,IAAI,EAAE,GAAG,CAAC,CAAA;QACV,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QAC1B,OAAO,EAAE,GAAG,EAAE,EAAE,CAAC;YACf,MAAM,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;YAC3B,IAAI,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,EAAE,CAAC;gBAC3B,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,EAAE,GAAG,GAAG,GAAG,CAAC,CAAA;YACd,CAAC;QACH,CAAC;QACD,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;YAC3B,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,UAAU,CAAC,EAAE,CAAE,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,UAAqC,EACrC,aAA4B;IAE5B,OAAO,CAAC,UAAU,IAAI,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;QAC3D,CAAC,CAAC,aAAa;QACf,CAAC,CAAC,UAAU,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,UAAsB;IACnD,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,OAAO,CAAC,CAAA;IACxC,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;QAC/B,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QACtC,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE,CAAC;YACf,MAAK;QACP,CAAC;QACD,IAAI,GAAG,GAAG,GAAG,EAAE,CAAC;YACd,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;YAC7D,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;YAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;QAClC,CAAC;QACD,GAAG,GAAG,GAAG,GAAG,CAAC,CAAA;QACb,SAAS,EAAE,CAAA;IACb,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,YAAY,GAA2B;IAC3C,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,MAAM,UAAU,YAAY,CAAC,KAAiB,EAAE,MAAc;IAC5D,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IACnD,MAAM,cAAc,GAClB,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;IACrE,MAAM,MAAM,GAAG,YAAY,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;IAC9C,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;IACrE,CAAC;IACD,MAAM,aAAa,GAAG;QACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;KAC1C,CAAA;IACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,cAAc,CACjD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;IACD,OAAO;QACL,WAAW;QACX,WAAW;QACX,SAAS;QACT,QAAQ;QACR,aAAa;QACb,MAAM;QACN,cAAc;KACf,CAAA;AACH,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO,EAAE,SAAS,EAAE,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC,EAAE,CAAA;AAC9D,CAAC;AAED,0DAA0D;AAC1D,MAAM,UAAU,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,GAAG,GAAG,IAAI,GAAG,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAC3C,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,MAAM,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC7B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QACxB,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/tabix",
|
|
3
|
-
"version": "3.4.
|
|
3
|
+
"version": "3.4.2",
|
|
4
4
|
"description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
|
|
5
5
|
"type": "module",
|
|
6
6
|
"main": "dist/index.js",
|
|
@@ -51,23 +51,23 @@
|
|
|
51
51
|
"@gmod/abortable-promise-cache": "^3.0.4",
|
|
52
52
|
"@gmod/bgzf-filehandle": "^6.2.0",
|
|
53
53
|
"@jbrowse/quick-lru": "^7.3.5",
|
|
54
|
-
"generic-filehandle2": "^2.
|
|
54
|
+
"generic-filehandle2": "^2.2.0"
|
|
55
55
|
},
|
|
56
56
|
"devDependencies": {
|
|
57
57
|
"@eslint/js": "^10.0.1",
|
|
58
|
-
"@types/node": "^25.9.
|
|
59
|
-
"@vitest/coverage-v8": "^4.1.
|
|
60
|
-
"eslint": "^10.
|
|
58
|
+
"@types/node": "^25.9.3",
|
|
59
|
+
"@vitest/coverage-v8": "^4.1.9",
|
|
60
|
+
"eslint": "^10.5.0",
|
|
61
61
|
"eslint-plugin-import-x": "^4.16.2",
|
|
62
62
|
"eslint-plugin-unicorn": "^64.0.0",
|
|
63
|
-
"prettier": "^3.8.
|
|
63
|
+
"prettier": "^3.8.4",
|
|
64
64
|
"rimraf": "^6.1.3",
|
|
65
65
|
"standard-changelog": "^7.0.1",
|
|
66
66
|
"typedoc": "^0.28.19",
|
|
67
67
|
"typedoc-plugin-markdown": "^4.12.0",
|
|
68
68
|
"typescript": "^6.0.3",
|
|
69
|
-
"typescript-eslint": "^8.
|
|
70
|
-
"vitest": "^4.1.
|
|
69
|
+
"typescript-eslint": "^8.61.1",
|
|
70
|
+
"vitest": "^4.1.9",
|
|
71
71
|
"webpack": "^5.107.2",
|
|
72
72
|
"webpack-cli": "^7.0.3"
|
|
73
73
|
},
|
package/src/chunk.ts
CHANGED
|
@@ -5,11 +5,22 @@ export default class Chunk {
|
|
|
5
5
|
public minv: VirtualOffset
|
|
6
6
|
public maxv: VirtualOffset
|
|
7
7
|
public bin: number
|
|
8
|
+
// Absolute byte offset where the fetch for this chunk ends. The compressed
|
|
9
|
+
// size of the final BGZF block (the one at maxv.blockPosition) is unknown
|
|
10
|
+
// from the index, so this defaults to a full max-size block past maxv. It can
|
|
11
|
+
// be tightened to the next known block boundary via clampChunkEnds.
|
|
12
|
+
public endPosition: number
|
|
8
13
|
|
|
9
|
-
constructor(
|
|
14
|
+
constructor(
|
|
15
|
+
minv: VirtualOffset,
|
|
16
|
+
maxv: VirtualOffset,
|
|
17
|
+
bin: number,
|
|
18
|
+
endPosition = maxv.blockPosition + (1 << 16),
|
|
19
|
+
) {
|
|
10
20
|
this.minv = minv
|
|
11
21
|
this.maxv = maxv
|
|
12
22
|
this.bin = bin
|
|
23
|
+
this.endPosition = endPosition
|
|
13
24
|
}
|
|
14
25
|
|
|
15
26
|
toString() {
|
|
@@ -19,6 +30,6 @@ export default class Chunk {
|
|
|
19
30
|
}
|
|
20
31
|
|
|
21
32
|
fetchedSize() {
|
|
22
|
-
return this.
|
|
33
|
+
return this.endPosition - this.minv.blockPosition
|
|
23
34
|
}
|
|
24
35
|
}
|
package/src/csi.ts
CHANGED
|
@@ -3,6 +3,7 @@ import { unzip } from '@gmod/bgzf-filehandle'
|
|
|
3
3
|
import Chunk from './chunk.ts'
|
|
4
4
|
import IndexFile from './indexFile.ts'
|
|
5
5
|
import {
|
|
6
|
+
clampChunkEnds,
|
|
6
7
|
findFirstData,
|
|
7
8
|
memoizeByRefId,
|
|
8
9
|
optimizeChunks,
|
|
@@ -44,7 +45,10 @@ export default class CSI extends IndexFile {
|
|
|
44
45
|
|
|
45
46
|
/** @internal */
|
|
46
47
|
async _parse(opts: Options = {}) {
|
|
47
|
-
const buf = await this.filehandle.readFile({
|
|
48
|
+
const buf = await this.filehandle.readFile({
|
|
49
|
+
signal: opts.signal,
|
|
50
|
+
onProgress: opts.onProgress,
|
|
51
|
+
})
|
|
48
52
|
const bytes = (await unzip(buf)) as Uint8Array
|
|
49
53
|
const dataView = new DataView(bytes.buffer)
|
|
50
54
|
|
|
@@ -133,6 +137,7 @@ export default class CSI extends IndexFile {
|
|
|
133
137
|
binIndex[bin] = chunks
|
|
134
138
|
}
|
|
135
139
|
}
|
|
140
|
+
clampChunkEnds(Object.values(binIndex).flat())
|
|
136
141
|
return { binIndex, stats }
|
|
137
142
|
}
|
|
138
143
|
|
package/src/indexFile.ts
CHANGED
|
@@ -4,6 +4,12 @@ import type { GenericFilehandle } from 'generic-filehandle2'
|
|
|
4
4
|
|
|
5
5
|
export interface Options {
|
|
6
6
|
signal?: AbortSignal
|
|
7
|
+
/**
|
|
8
|
+
* Called as the index (.tbi/.csi) is downloaded, with cumulative downloaded
|
|
9
|
+
* bytes and the total. The index is a whole-file read, so this streams real
|
|
10
|
+
* byte progress. Lets callers show a determinate "downloading index" bar.
|
|
11
|
+
*/
|
|
12
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
|
|
7
13
|
}
|
|
8
14
|
|
|
9
15
|
export interface RefIndex {
|
package/src/tabixIndexedFile.ts
CHANGED
|
@@ -33,7 +33,7 @@ interface GetLinesOpts {
|
|
|
33
33
|
* which is the natural unit since chunk byte sizes are known up front from
|
|
34
34
|
* the index. Lets callers render a determinate download progress bar.
|
|
35
35
|
*/
|
|
36
|
-
onProgress?: (bytesDownloaded: number, totalBytes
|
|
36
|
+
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
|
|
37
37
|
}
|
|
38
38
|
|
|
39
39
|
interface ReadChunk {
|
package/src/tbi.ts
CHANGED
|
@@ -3,6 +3,7 @@ import { unzip } from '@gmod/bgzf-filehandle'
|
|
|
3
3
|
import Chunk from './chunk.ts'
|
|
4
4
|
import IndexFile from './indexFile.ts'
|
|
5
5
|
import {
|
|
6
|
+
clampChunkEnds,
|
|
6
7
|
findFirstData,
|
|
7
8
|
memoizeByRefId,
|
|
8
9
|
optimizeChunks,
|
|
@@ -36,7 +37,10 @@ function reg2bins(beg: number, end: number) {
|
|
|
36
37
|
export default class TabixIndex extends IndexFile {
|
|
37
38
|
/** @internal */
|
|
38
39
|
async _parse(opts: Options = {}) {
|
|
39
|
-
const buf = await this.filehandle.readFile({
|
|
40
|
+
const buf = await this.filehandle.readFile({
|
|
41
|
+
signal: opts.signal,
|
|
42
|
+
onProgress: opts.onProgress,
|
|
43
|
+
})
|
|
40
44
|
const bytes = (await unzip(buf)) as Uint8Array
|
|
41
45
|
const dataView = new DataView(bytes.buffer)
|
|
42
46
|
|
|
@@ -144,6 +148,10 @@ export default class TabixIndex extends IndexFile {
|
|
|
144
148
|
linearIndex[k] = fromBytes(bytes, pos)
|
|
145
149
|
pos += 8
|
|
146
150
|
}
|
|
151
|
+
clampChunkEnds(
|
|
152
|
+
Object.values(binIndex).flat(),
|
|
153
|
+
linearIndex.map(v => v.blockPosition),
|
|
154
|
+
)
|
|
147
155
|
return { binIndex, linearIndex, stats }
|
|
148
156
|
}
|
|
149
157
|
|