@gmod/tabix 3.8.3 → 3.9.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +11 -0
- package/dist/csi.js +4 -1
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.js +12 -2
- package/dist/indexFile.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.js +149 -63
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/util.js +1 -0
- package/dist/util.js.map +1 -1
- package/esm/csi.js +4 -1
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.js +12 -2
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.js +149 -63
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/util.js +1 -0
- package/esm/util.js.map +1 -1
- package/package.json +3 -3
- package/src/csi.ts +4 -1
- package/src/indexFile.ts +13 -2
- package/src/tabixIndexedFile.ts +212 -87
- package/src/util.ts +1 -0
package/README.md
CHANGED
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@@ -107,6 +107,17 @@ Notes:
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if a query comes back unexpectedly empty
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- `start > end` throws a `TypeError`; `start === end` returns without reading
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+
### GAF
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+
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Reads `tabix -p gaf` indexes of sorted GAF (e.g. from `vg gamsort`):
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+
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- `refName` is ignored; `getReferenceSequenceNames()` returns `[]`
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+
- `start`/`end` are node ids: a read matches when its lowest-to-highest node
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range `[min, max]` touches any of `start..end-1`, the same reads as
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`tabix file.gaf.gz "{x}:start-end"` (no `+1`)
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- The callback gets `min` and `max + 1`
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- Reads whose path is a stable sequence name (no `>`/`<`) are skipped
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+
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### Without NPM (CDN)
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```html
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package/dist/csi.js
CHANGED
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@@ -37,7 +37,10 @@ class CSI extends indexFile_ts_1.default {
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const maxBinNumber = (8 ** (depth + 1) - 1) / 7;
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const maxRefLength = 2 ** (minShift + depth * 3);
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const auxLength = dataView.getInt32(12, true);
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-
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+
// htslib names no references in a GAF index, so its aux is the bare
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// 28-byte header block
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const isGaf = auxLength >= 28 && (dataView.getInt32(16, true) & 0xf) === 3;
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const aux = auxLength >= 30 || isGaf
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? (0, util_ts_1.parseAuxData)(bytes, 16)
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: {
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refIdToName: [],
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package/dist/csi.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,0DAA8B;AAC9B,kEAAsC;AACtC,uCAMkB;AAClB,yDAA8C;AAK9C,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,MAAqB,GAAI,SAAQ,sBAAS;IACxC,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAE3D,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,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC/C,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,QAAQ,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAChD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GACP,SAAS,IAAI,EAAE;
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1
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+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,0DAA8B;AAC9B,kEAAsC;AACtC,uCAMkB;AAClB,yDAA8C;AAK9C,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,MAAqB,GAAI,SAAQ,sBAAS;IACxC,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAE3D,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,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC/C,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,QAAQ,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAChD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,oEAAoE;QACpE,uBAAuB;QACvB,MAAM,KAAK,GAAG,SAAS,IAAI,EAAE,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC,CAAA;QAC1E,MAAM,GAAG,GACP,SAAS,IAAI,EAAE,IAAI,KAAK;YACtB,CAAC,CAAC,IAAA,sBAAY,EAAC,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,IAAA,0BAAgB,EAAC,KAAK,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,CAAC,CAAA;oBAC/D,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,MAAM,QAAQ,GAAkC,EAAE,CAAA;YAClD,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,IAAA,wBAAc,EAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACvC,GAAG,IAAI,EAAE,GAAG,EAAE,CAAA;gBAChB,CAAC;qBAAM,CAAC;oBACN,QAAQ,CAAC,GAAG,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,CAAA;oBACrC,GAAG,IAAI,CAAC,CAAA;oBACR,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,IAAA,wBAAc,EAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACtC,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,IAAA,wBAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;YACR,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAA;IACH,CAAC;IAED;;;;;;OAMG;IACO,YAAY,CACpB,GAAa,EACb,GAAW,EACX,EAAE,QAAQ,EAAE,KAAK,EAAa;QAE9B,MAAM,EAAE,QAAQ,EAAE,GAAG,GAAG,CAAA;QACxB,IAAI,KAAgC,CAAA;QACpC,IAAI,QAAQ,EAAE,CAAC;YACb,0DAA0D;YAC1D,IAAI,GAAG,GACL,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACrE,OAAO,KAAK,KAAK,SAAS,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACtC,KAAK,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACrB,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;oBACxB,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBACxC,MAAM,UAAU,GAAG,MAAM,GAAG,CAAC,GAAG,CAAC,CAAA;oBACjC,GAAG,GAAG,GAAG,GAAG,UAAU,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,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package/dist/indexFile.js
CHANGED
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@@ -48,6 +48,10 @@ function maxOffset(binIndex, end, minShift, depth) {
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bin++;
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}
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}
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// htslib files every GAF record under ref 0 and ignores a query's name
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function refIdFor(indexData, refName) {
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return indexData.format === 'GAF' ? 0 : indexData.refNameToId[refName];
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}
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class IndexFile {
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filehandle;
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/**
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/** @internal */
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async lineCount(refName, opts = {}) {
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const indexData = await this.parse(opts);
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const refId = indexData
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const refId = refIdFor(indexData, refName);
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*/
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async blocksForRange(refName, min, max, opts = {}) {
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const refId = indexData
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const refId = refIdFor(indexData, refName);
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return [];
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}
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if (!ba) {
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return [];
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}
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// htslib indexes a GAF read as [minNode, maxNode), one short of the
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// [minNode, maxNode] that getLines matches, so look one node lower, as
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// `tabix` does for a region's 1-based start
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if (indexData.format === 'GAF') {
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min = Math.max(min - 1, 0);
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}
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// Find chunks in overlapping bins. Leaf bins are not pruned.
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const chunks = [];
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for (const [start, end] of this.reg2bins(min, max, indexData)) {
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package/dist/indexFile.js.map
CHANGED
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@@ -1 +1 @@
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-
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