@gmod/tabix 3.4.1 → 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 +1 -0
- package/dist/csi.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tbi.js +1 -0
- 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 +2 -1
- package/esm/csi.js.map +1 -1
- package/esm/tbi.js +2 -1
- 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 +1 -1
- package/src/chunk.ts +13 -2
- package/src/csi.ts +2 -0
- package/src/tbi.ts +5 -0
- package/src/util.ts +34 -0
package/dist/tbi.js
CHANGED
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@@ -121,6 +121,7 @@ class TabixIndex extends indexFile_ts_1.default {
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121
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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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124
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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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export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
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4
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+
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
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5
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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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@@ -73,6 +74,38 @@ function optimizeChunks(chunks, lowest) {
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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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83
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// Shrinks both the byte estimate and the actual fetch with no extra I/O.
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84
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+
function clampChunkEnds(chunks, extraBoundaries = []) {
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85
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+
const boundaries = [...extraBoundaries];
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86
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+
for (const c of chunks) {
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87
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boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
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}
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89
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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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95
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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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@@ -1 +1 @@
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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;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|
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
|
|
@@ -115,6 +115,7 @@ export default class CSI extends IndexFile {
|
|
|
115
115
|
binIndex[bin] = chunks;
|
|
116
116
|
}
|
|
117
117
|
}
|
|
118
|
+
clampChunkEnds(Object.values(binIndex).flat());
|
|
118
119
|
return { binIndex, stats };
|
|
119
120
|
}
|
|
120
121
|
return {
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
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
|
/**
|
|
@@ -116,6 +116,7 @@ export default class TabixIndex extends IndexFile {
|
|
|
116
116
|
linearIndex[k] = fromBytes(bytes, pos);
|
|
117
117
|
pos += 8;
|
|
118
118
|
}
|
|
119
|
+
clampChunkEnds(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
|
|
119
120
|
return { binIndex, linearIndex, stats };
|
|
120
121
|
}
|
|
121
122
|
return {
|
package/esm/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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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;I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|
package/package.json
CHANGED
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,
|
|
@@ -136,6 +137,7 @@ export default class CSI extends IndexFile {
|
|
|
136
137
|
binIndex[bin] = chunks
|
|
137
138
|
}
|
|
138
139
|
}
|
|
140
|
+
clampChunkEnds(Object.values(binIndex).flat())
|
|
139
141
|
return { binIndex, stats }
|
|
140
142
|
}
|
|
141
143
|
|
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,
|
|
@@ -147,6 +148,10 @@ export default class TabixIndex extends IndexFile {
|
|
|
147
148
|
linearIndex[k] = fromBytes(bytes, pos)
|
|
148
149
|
pos += 8
|
|
149
150
|
}
|
|
151
|
+
clampChunkEnds(
|
|
152
|
+
Object.values(binIndex).flat(),
|
|
153
|
+
linearIndex.map(v => v.blockPosition),
|
|
154
|
+
)
|
|
150
155
|
return { binIndex, linearIndex, stats }
|
|
151
156
|
}
|
|
152
157
|
|
package/src/util.ts
CHANGED
|
@@ -65,6 +65,7 @@ export function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset) {
|
|
|
65
65
|
lastChunk.minv,
|
|
66
66
|
chunk.maxv,
|
|
67
67
|
lastChunk.bin,
|
|
68
|
+
chunk.endPosition,
|
|
68
69
|
)
|
|
69
70
|
lastMaxBlock = chunkMaxBlock
|
|
70
71
|
}
|
|
@@ -78,6 +79,39 @@ export function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset) {
|
|
|
78
79
|
return mergedChunks
|
|
79
80
|
}
|
|
80
81
|
|
|
82
|
+
// Tighten each chunk's endPosition (default: a full max-size BGZF block past
|
|
83
|
+
// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
|
|
84
|
+
// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
|
|
85
|
+
// since blocks don't overlap, the first boundary strictly greater than a chunk's
|
|
86
|
+
// maxv.blockPosition is an upper bound on where that final block ends — always at
|
|
87
|
+
// least the true block end, so the clamped fetch still contains the whole block.
|
|
88
|
+
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
89
|
+
export function clampChunkEnds(chunks: Chunk[], extraBoundaries: number[] = []) {
|
|
90
|
+
const boundaries = [...extraBoundaries]
|
|
91
|
+
for (const c of chunks) {
|
|
92
|
+
boundaries.push(c.minv.blockPosition, c.maxv.blockPosition)
|
|
93
|
+
}
|
|
94
|
+
boundaries.sort((a, b) => a - b)
|
|
95
|
+
|
|
96
|
+
for (const c of chunks) {
|
|
97
|
+
const max = c.maxv.blockPosition
|
|
98
|
+
// first boundary strictly greater than max
|
|
99
|
+
let lo = 0
|
|
100
|
+
let hi = boundaries.length
|
|
101
|
+
while (lo < hi) {
|
|
102
|
+
const mid = (lo + hi) >>> 1
|
|
103
|
+
if (boundaries[mid]! > max) {
|
|
104
|
+
hi = mid
|
|
105
|
+
} else {
|
|
106
|
+
lo = mid + 1
|
|
107
|
+
}
|
|
108
|
+
}
|
|
109
|
+
if (lo < boundaries.length) {
|
|
110
|
+
c.endPosition = Math.min(c.endPosition, boundaries[lo]!)
|
|
111
|
+
}
|
|
112
|
+
}
|
|
113
|
+
}
|
|
114
|
+
|
|
81
115
|
export function findFirstData(
|
|
82
116
|
currentFdl: VirtualOffset | undefined,
|
|
83
117
|
virtualOffset: VirtualOffset,
|