@gmod/tabix 1.5.0 → 1.5.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +7 -0
- package/README.md +3 -2
- package/dist/chunk.js +33 -62
- package/dist/csi.d.ts +0 -1
- package/dist/csi.js +324 -533
- package/dist/index.js +11 -36
- package/dist/indexFile.d.ts +1 -1
- package/dist/indexFile.js +112 -174
- package/dist/tabixIndexedFile.d.ts +8 -4
- package/dist/tabixIndexedFile.js +476 -774
- package/dist/tbi.js +308 -485
- package/dist/util.js +132 -148
- package/dist/virtualOffset.js +44 -68
- package/esm/chunk.d.ts +18 -0
- package/esm/chunk.js +35 -0
- package/esm/csi.d.ts +71 -0
- package/esm/csi.js +254 -0
- package/esm/index.d.ts +4 -0
- package/esm/index.js +12 -0
- package/esm/indexFile.d.ts +32 -0
- package/esm/indexFile.js +45 -0
- package/esm/tabixIndexedFile.d.ts +118 -0
- package/esm/tabixIndexedFile.js +403 -0
- package/esm/tbi.d.ts +45 -0
- package/esm/tbi.js +240 -0
- package/esm/util.d.ts +25 -0
- package/esm/util.js +98 -0
- package/esm/virtualOffset.d.ts +10 -0
- package/esm/virtualOffset.js +41 -0
- package/package.json +23 -40
- package/dist/declare.d.js +0 -2
package/CHANGELOG.md
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<a name="1.5.1"></a>
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## [1.5.1](https://github.com/GMOD/tabix-js/compare/v1.5.0...v1.5.1) (2021-12-15)
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- Add esm module with less babelification for smaller bundle size
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<a name="1.5.0"></a>
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# [1.5.0](https://github.com/GMOD/tabix-js/compare/v1.4.6...v1.5.0) (2020-12-11)
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package/README.md
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# @gmod/tabix
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[](https://npmjs.org/package/@gmod/tabix)
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[](https://codecov.io/gh/GMOD/tabix-js/branch/master)
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[](https://github.com/GMOD/tabix-js/actions?query=branch%3Amaster+workflow%3APush+)
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Read Tabix-indexed files using either .tbi or .csi indexes.
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package/dist/chunk.js
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"use strict";
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var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");
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var _Object$defineProperty = require("@babel/runtime-corejs2/core-js/object/define-property");
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_Object$defineProperty(exports, "__esModule", {
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value: true
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});
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exports.default = void 0;
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var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));
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var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));
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var _defineProperty2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/defineProperty"));
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Object.defineProperty(exports, "__esModule", { value: true });
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// little class representing a chunk in the index
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var Chunk =
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(0, _defineProperty2.default)(this, "_fetchedSize", void 0);
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this.minv = minv;
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this.maxv = maxv;
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this.bin = bin;
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this._fetchedSize = fetchedSize;
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}
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(0, _createClass2.default)(Chunk, [{
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key: "toUniqueString",
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value: function toUniqueString() {
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return "".concat(this.minv, "..").concat(this.maxv, " (bin ").concat(this.bin, ", fetchedSize ").concat(this.fetchedSize(), ")");
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var Chunk = /** @class */ (function () {
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/**
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* @param {VirtualOffset} minv
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* @param {VirtualOffset} maxv
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* @param {number} bin
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* @param {number} [fetchedSize]
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*/
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function Chunk(minv, maxv, bin, fetchedSize) {
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if (fetchedSize === void 0) { fetchedSize = undefined; }
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this.minv = minv;
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this.maxv = maxv;
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this.bin = bin;
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this._fetchedSize = fetchedSize;
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}
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}();
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Chunk.prototype.toUniqueString = function () {
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return "".concat(this.minv, "..").concat(this.maxv, " (bin ").concat(this.bin, ", fetchedSize ").concat(this.fetchedSize(), ")");
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};
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Chunk.prototype.toString = function () {
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return this.toUniqueString();
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};
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Chunk.prototype.compareTo = function (b) {
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return (this.minv.compareTo(b.minv) ||
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this.maxv.compareTo(b.maxv) ||
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this.bin - b.bin);
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};
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Chunk.prototype.fetchedSize = function () {
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if (this._fetchedSize !== undefined) {
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return this._fetchedSize;
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}
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return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition;
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};
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return Chunk;
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}());
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exports.default = Chunk;
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//# sourceMappingURL=data:application/json;charset=utf-8;base64,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package/dist/csi.d.ts
CHANGED
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blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
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/**
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* calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
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*/
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reg2bins(beg: number, end: number): number[][];
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}
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