@jbrowse/plugin-gff3 2.1.0 → 2.1.2
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/Gff3Adapter/Gff3Adapter.js +85 -228
- package/dist/Gff3Adapter/Gff3Adapter.js.map +1 -1
- package/dist/Gff3Adapter/configSchema.js +1 -1
- package/dist/Gff3Adapter/configSchema.js.map +1 -1
- package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js +113 -235
- package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js.map +1 -1
- package/dist/Gff3TabixAdapter/configSchema.js +2 -2
- package/dist/Gff3TabixAdapter/configSchema.js.map +1 -1
- package/dist/index.js +34 -60
- package/dist/index.js.map +1 -1
- package/package.json +2 -3
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const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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const io_1 = require("@jbrowse/core/util/io");
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const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
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const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const gff_1 = __importDefault(require("@gmod/gff"));
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_b.label = 4;
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data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
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}
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header = headerLines.join('\n');
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feats = gff_1.default.parseStringSync(data, {
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parseFeatures: true,
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parseComments: false,
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intervalTree = feats
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.flat()
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.map(function (f, i) {
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return new simpleFeature_1.default({
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data: _this.featureData(f),
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id: "".concat(_this.id, "-offset-").concat(i),
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.reduce(function (acc, obj) {
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if (!acc[key]) {
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acc[key] = new interval_tree_1.default();
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}
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acc[key].insert([obj.get('start'), obj.get('end')], obj);
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return acc;
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}, {});
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return [2 /*return*/, { header: header, intervalTree: intervalTree }];
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});
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});
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};
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default_1.prototype.loadData = function () {
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throw e;
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}
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});
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};
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default_1.prototype.getRefNames = function (opts) {
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if (opts === void 0) { opts = {}; }
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return __awaiter(this, void 0, void 0, function () {
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var intervalTree;
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return __generator(this, function (_a) {
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switch (_a.label) {
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case 0: return [4 /*yield*/, this.loadData()];
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case 1:
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intervalTree = (_a.sent()).intervalTree;
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return [2 /*return*/, Object.keys(intervalTree)];
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}
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});
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class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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async loadDataP() {
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const pm = this.pluginManager;
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const buf = await (0, io_1.openLocation)(this.getConf('gffLocation'), pm).readFile();
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const buffer = isGzip(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
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// 512MB max chrome string length is 512MB
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if (buffer.length > 536870888) {
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throw new Error('Data exceeds maximum string length (512MB)');
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}
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const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
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const lines = data.split('\n');
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const headerLines = [];
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for (let i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
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headerLines.push(lines[i]);
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}
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const header = headerLines.join('\n');
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const feats = gff_1.default.parseStringSync(data, {
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parseFeatures: true,
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parseComments: false,
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parseDirectives: false,
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parseSequences: false,
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});
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const intervalTree = feats
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.flat()
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.map((f, i) => new simpleFeature_1.default({
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data: this.featureData(f),
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id: `${this.id}-offset-${i}`,
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}))
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.reduce((acc, obj) => {
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const key = obj.get('refName');
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if (!acc[key]) {
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acc[key] = new interval_tree_1.default();
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}
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acc[key].insert([obj.get('start'), obj.get('end')], obj);
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return acc;
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}, {});
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return { header, intervalTree };
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}
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async loadData() {
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if (!this.gffFeatures) {
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this.gffFeatures = this.loadDataP().catch(e => {
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this.gffFeatures = undefined;
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throw e;
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});
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}
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return this.gffFeatures;
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}
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async getRefNames(opts = {}) {
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const { intervalTree } = await this.loadData();
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return Object.keys(intervalTree);
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}
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async getHeader() {
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const { header } = await this.loadData();
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return header;
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}
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getFeatures(query, opts = {}) {
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}); }, opts.signal);
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};
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default_1.prototype.featureData = function (data) {
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var f = __assign({}, data);
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try {
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const { start, end, refName } = query;
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const { intervalTree } = await this.loadData();
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(_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(f));
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observer.complete();
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}
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catch (e) {
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}
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}, opts.signal);
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}
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featureData(data) {
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const f = { ...data };
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@@ -246,7 +105,7 @@ var default_1 = /** @class */ (function (_super) {
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{"version":3,"file":"Gff3Adapter.js","sourceRoot":"","sources":["../../src/Gff3Adapter/Gff3Adapter.ts"],"names":[],"mappings":"
|
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+
{"version":3,"file":"Gff3Adapter.js","sourceRoot":"","sources":["../../src/Gff3Adapter/Gff3Adapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,qFAAyE;AACzE,2DAA6C;AAE7C,oDAAwD;AAExD,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,eAAqB,SAAQ,oCAAsB;IAMzC,KAAK,CAAC,SAAS;QACrB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAC1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC9B,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACjE,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAErC,MAAM,KAAK,GAAG,aAAG,CAAC,eAAe,CAAC,IAAI,EAAE;YACtC,aAAa,EAAE,IAAI;YACnB,aAAa,EAAE,KAAK;YACpB,eAAe,EAAE,KAAK;YACtB,cAAc,EAAE,KAAK;SACtB,CAAC,CAAA;QAEF,MAAM,YAAY,GAAG,KAAK;aACvB,IAAI,EAAE;aACN,GAAG,CACF,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,IAAI,uBAAa,CAAC;YAChB,IAAI,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC;YACzB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,EAAE;SAC7B,CAAC,CACL;aACA,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YAC9B,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YACxD,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEO,KAAK,CAAC,QAAQ;QACpB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC5C,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACxC,OAAO,MAAM,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;gBACrC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;gBAC9C,MAAA,YAAY,CAAC,OAAO,CAAC,0CACjB,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EACpB,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;gBACjC,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,WAAW,CAAC,IAA6B;QAC/C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;QAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;QACjD,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YACvB,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SACd;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM;YACL,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;SACrB;QACD,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QACvB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,MAAM,aAAa,GAAG;YACpB,OAAO;YACP,KAAK;YACL,QAAQ;YACR,OAAO;YACP,MAAM;YACN,QAAQ;YACR,OAAO;YACP,QAAQ;SACT,CAAA;QACD,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAA;QAC5C,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACtC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;YACvB,IAAI,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE;gBAC7B,gDAAgD;gBAChD,gCAAgC;gBAChC,CAAC,IAAI,GAAG,CAAA;aACT;YACD,IAAI,cAAc,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;gBAC9B,IAAI,IAAI,GAAkC,cAAc,CAAC,CAAC,CAAC,CAAA;gBAC3D,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;oBAC5C,CAAC;oBAAA,CAAC,IAAI,CAAC,GAAG,IAAI,CAAA;iBACf;gBACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;aACZ;QACH,CAAC,CAAC,CAAA;QACF,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,CAAA;QAEpB,gFAAgF;QAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE;YACrD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc;iBAChC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;iBACvE,IAAI,EAAE,CAAA;SACV;QAED,OAAO,CAAC,CAAC,cAAc,CAAA;QACvB,OAAO,CAAC,CAAC,IAAI,CAAA;QACb,OAAO,CAAC,CAAC,gBAAgB,CAAA;QACzB,OAAO,CAAC,CAAC,UAAU,CAAA;QACnB,OAAO,CAAC,CAAC,MAAM,CAAA;QACf,OAAO,CAAC,CAAA;IACV,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAG,CAAC;CAC1C;AAtJD,4BAsJC"}
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"use strict";
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|
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|
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|
+
const configuration_1 = require("@jbrowse/core/configuration");
|
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4
|
exports.default = (0, configuration_1.ConfigurationSchema)('Gff3Adapter', {
|
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gffLocation: {
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3Adapter/configSchema.ts"],"names":[],"mappings":";;AAAA
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3Adapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,aAAa,EACb;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
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filehandle: (0, io_1.openLocation)(gffGzLocation, _this.pluginManager),
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const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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const range_1 = require("@jbrowse/core/util/range");
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const io_1 = require("@jbrowse/core/util/io");
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const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
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const tabix_1 = require("@gmod/tabix");
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const gff_1 = __importDefault(require("@gmod/gff"));
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const configuration_1 = require("@jbrowse/core/configuration");
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class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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+
constructor(config, getSubAdapter, pluginManager) {
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super(config, getSubAdapter, pluginManager);
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const gffGzLocation = (0, configuration_1.readConfObject)(config, 'gffGzLocation');
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const indexType = (0, configuration_1.readConfObject)(config, ['index', 'indexType']);
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const location = (0, configuration_1.readConfObject)(config, ['index', 'location']);
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const dontRedispatch = (0, configuration_1.readConfObject)(config, 'dontRedispatch');
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this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region'];
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this.gff = new tabix_1.TabixIndexedFile({
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filehandle: (0, io_1.openLocation)(gffGzLocation, this.pluginManager),
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csiFilehandle: indexType === 'CSI'
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? (0, io_1.openLocation)(location,
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? (0, io_1.openLocation)(location, this.pluginManager)
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: undefined,
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tbiFilehandle: indexType !== 'CSI'
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? (0, io_1.openLocation)(location,
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? (0, io_1.openLocation)(location, this.pluginManager)
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: undefined,
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chunkCacheSize: 50 *
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renameRefSeqs:
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chunkCacheSize: 50 * 2 ** 20,
|
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|
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renameRefSeqs: (n) => n,
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33
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});
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|
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return _this;
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}
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|
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if (opts === void 0) { opts = {}; }
|
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|
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return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
|
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|
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var metadata;
|
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|
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return __generator(this, function (_a) {
|
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|
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switch (_a.label) {
|
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|
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case 0: return [4 /*yield*/, this.gff.getMetadata()];
|
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|
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case 1:
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|
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metadata = _a.sent();
|
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|
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this.getFeaturesHelper(query, opts, metadata, observer, true);
|
|
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|
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return [2 /*return*/];
|
|
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|
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}
|
|
35
|
+
async getRefNames(opts = {}) {
|
|
36
|
+
return this.gff.getReferenceSequenceNames(opts);
|
|
37
|
+
}
|
|
38
|
+
async getHeader() {
|
|
39
|
+
return this.gff.getHeader();
|
|
40
|
+
}
|
|
41
|
+
getFeatures(query, opts = {}) {
|
|
42
|
+
return (0, rxjs_1.ObservableCreate)(async (observer) => {
|
|
43
|
+
const metadata = await this.gff.getMetadata();
|
|
44
|
+
this.getFeaturesHelper(query, opts, metadata, observer, true);
|
|
45
|
+
}, opts.signal);
|
|
46
|
+
}
|
|
47
|
+
async getFeaturesHelper(query, opts = {}, metadata, observer, allowRedispatch, originalQuery = query) {
|
|
48
|
+
try {
|
|
49
|
+
const lines = [];
|
|
50
|
+
await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
|
|
51
|
+
lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
|
|
143
52
|
});
|
|
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|
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|
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|
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|
|
154
|
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|
|
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|
-
_a.trys.push([0, 2, , 3]);
|
|
156
|
-
lines_1 = [];
|
|
157
|
-
return [4 /*yield*/, this.gff.getLines(query.refName, query.start, query.end, function (line, fileOffset) {
|
|
158
|
-
lines_1.push(_this.parseLine(metadata.columnNumbers, line, fileOffset));
|
|
159
|
-
})];
|
|
160
|
-
case 1:
|
|
161
|
-
_a.sent();
|
|
162
|
-
if (allowRedispatch && lines_1.length) {
|
|
163
|
-
minStart_1 = Infinity;
|
|
164
|
-
maxEnd_1 = -Infinity;
|
|
165
|
-
lines_1.forEach(function (line) {
|
|
166
|
-
var featureType = line.fields[2];
|
|
167
|
-
// only expand redispatch range if feature is not a "dontRedispatch" type
|
|
168
|
-
// skips large regions like chromosome,region
|
|
169
|
-
if (!_this.dontRedispatch.includes(featureType)) {
|
|
170
|
-
var start = line.start - 1; // gff is 1-based
|
|
171
|
-
if (start < minStart_1) {
|
|
172
|
-
minStart_1 = start;
|
|
173
|
-
}
|
|
174
|
-
if (line.end > maxEnd_1) {
|
|
175
|
-
maxEnd_1 = line.end;
|
|
176
|
-
}
|
|
177
|
-
}
|
|
178
|
-
});
|
|
179
|
-
if (maxEnd_1 > query.end || minStart_1 < query.start) {
|
|
180
|
-
// make a new feature callback to only return top-level features
|
|
181
|
-
// in the original query range
|
|
182
|
-
this.getFeaturesHelper(__assign(__assign({}, query), { start: minStart_1, end: maxEnd_1 }), opts, metadata, observer, false, query);
|
|
183
|
-
return [2 /*return*/];
|
|
184
|
-
}
|
|
53
|
+
if (allowRedispatch && lines.length) {
|
|
54
|
+
let minStart = Infinity;
|
|
55
|
+
let maxEnd = -Infinity;
|
|
56
|
+
lines.forEach(line => {
|
|
57
|
+
const featureType = line.fields[2];
|
|
58
|
+
// only expand redispatch range if feature is not a "dontRedispatch" type
|
|
59
|
+
// skips large regions like chromosome,region
|
|
60
|
+
if (!this.dontRedispatch.includes(featureType)) {
|
|
61
|
+
const start = line.start - 1; // gff is 1-based
|
|
62
|
+
if (start < minStart) {
|
|
63
|
+
minStart = start;
|
|
185
64
|
}
|
|
186
|
-
|
|
187
|
-
|
|
188
|
-
|
|
189
|
-
|
|
190
|
-
|
|
191
|
-
|
|
192
|
-
|
|
193
|
-
|
|
194
|
-
|
|
195
|
-
|
|
196
|
-
return lineRecord.fields.join('\t');
|
|
197
|
-
})
|
|
198
|
-
.join('\n');
|
|
199
|
-
features = gff_1.default.parseStringSync(gff3, {
|
|
200
|
-
parseFeatures: true,
|
|
201
|
-
parseComments: false,
|
|
202
|
-
parseDirectives: false,
|
|
203
|
-
parseSequences: false,
|
|
204
|
-
});
|
|
205
|
-
features.forEach(function (featureLocs) {
|
|
206
|
-
return _this.formatFeatures(featureLocs).forEach(function (f) {
|
|
207
|
-
if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
|
|
208
|
-
observer.next(f);
|
|
209
|
-
}
|
|
210
|
-
});
|
|
211
|
-
});
|
|
212
|
-
observer.complete();
|
|
213
|
-
return [3 /*break*/, 3];
|
|
214
|
-
case 2:
|
|
215
|
-
e_1 = _a.sent();
|
|
216
|
-
observer.error(e_1);
|
|
217
|
-
return [3 /*break*/, 3];
|
|
218
|
-
case 3: return [2 /*return*/];
|
|
65
|
+
if (line.end > maxEnd) {
|
|
66
|
+
maxEnd = line.end;
|
|
67
|
+
}
|
|
68
|
+
}
|
|
69
|
+
});
|
|
70
|
+
if (maxEnd > query.end || minStart < query.start) {
|
|
71
|
+
// make a new feature callback to only return top-level features
|
|
72
|
+
// in the original query range
|
|
73
|
+
this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
|
|
74
|
+
return;
|
|
219
75
|
}
|
|
76
|
+
}
|
|
77
|
+
const gff3 = lines
|
|
78
|
+
.map((lineRecord) => {
|
|
79
|
+
if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
|
|
80
|
+
if (!lineRecord.fields[8].includes('_lineHash')) {
|
|
81
|
+
lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
|
|
82
|
+
}
|
|
83
|
+
}
|
|
84
|
+
else {
|
|
85
|
+
lineRecord.fields[8] = `_lineHash=${lineRecord.lineHash}`;
|
|
86
|
+
}
|
|
87
|
+
return lineRecord.fields.join('\t');
|
|
88
|
+
})
|
|
89
|
+
.join('\n');
|
|
90
|
+
const features = gff_1.default.parseStringSync(gff3, {
|
|
91
|
+
parseFeatures: true,
|
|
92
|
+
parseComments: false,
|
|
93
|
+
parseDirectives: false,
|
|
94
|
+
parseSequences: false,
|
|
220
95
|
});
|
|
221
|
-
|
|
222
|
-
|
|
223
|
-
|
|
224
|
-
|
|
96
|
+
features.forEach(featureLocs => this.formatFeatures(featureLocs).forEach(f => {
|
|
97
|
+
if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
|
|
98
|
+
observer.next(f);
|
|
99
|
+
}
|
|
100
|
+
}));
|
|
101
|
+
observer.complete();
|
|
102
|
+
}
|
|
103
|
+
catch (e) {
|
|
104
|
+
observer.error(e);
|
|
105
|
+
}
|
|
106
|
+
}
|
|
107
|
+
parseLine(columnNumbers, line, fileOffset) {
|
|
108
|
+
const fields = line.split('\t');
|
|
225
109
|
// note: index column numbers are 1-based
|
|
226
110
|
return {
|
|
227
111
|
start: +fields[columnNumbers.start - 1],
|
|
228
112
|
end: +fields[columnNumbers.end - 1],
|
|
229
113
|
lineHash: fileOffset,
|
|
230
|
-
fields
|
|
114
|
+
fields,
|
|
231
115
|
};
|
|
232
|
-
}
|
|
233
|
-
|
|
234
|
-
|
|
235
|
-
|
|
236
|
-
|
|
237
|
-
|
|
238
|
-
|
|
239
|
-
|
|
240
|
-
|
|
241
|
-
}
|
|
242
|
-
};
|
|
243
|
-
default_1.prototype.featureData = function (data) {
|
|
244
|
-
var _this = this;
|
|
245
|
-
var f = __assign({}, data);
|
|
116
|
+
}
|
|
117
|
+
formatFeatures(featureLocs) {
|
|
118
|
+
return featureLocs.map(featureLoc => new simpleFeature_1.default({
|
|
119
|
+
data: this.featureData(featureLoc),
|
|
120
|
+
// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
|
|
121
|
+
id: `${this.id}-offset-${featureLoc.attributes._lineHash[0]}`,
|
|
122
|
+
}));
|
|
123
|
+
}
|
|
124
|
+
featureData(data) {
|
|
125
|
+
const f = { ...data };
|
|
246
126
|
f.start -= 1; // convert to interbase
|
|
247
127
|
if (data.strand === '+') {
|
|
248
128
|
f.strand = 1;
|
|
@@ -264,7 +144,7 @@ var default_1 = /** @class */ (function (_super) {
|
|
|
264
144
|
if (data.phase === null) {
|
|
265
145
|
delete f.score;
|
|
266
146
|
}
|
|
267
|
-
|
|
147
|
+
const defaultFields = [
|
|
268
148
|
'start',
|
|
269
149
|
'end',
|
|
270
150
|
'seq_id',
|
|
@@ -274,20 +154,19 @@ var default_1 = /** @class */ (function (_super) {
|
|
|
274
154
|
'phase',
|
|
275
155
|
'strand',
|
|
276
156
|
];
|
|
277
|
-
|
|
278
|
-
Object.keys(dataAttributes).forEach(
|
|
279
|
-
|
|
280
|
-
var b = a.toLowerCase();
|
|
157
|
+
const dataAttributes = data.attributes || {};
|
|
158
|
+
Object.keys(dataAttributes).forEach(a => {
|
|
159
|
+
let b = a.toLowerCase();
|
|
281
160
|
if (defaultFields.includes(b)) {
|
|
282
161
|
// add "suffix" to tag name if it already exists
|
|
283
162
|
// reproduces behavior of NCList
|
|
284
163
|
b += '2';
|
|
285
164
|
}
|
|
286
165
|
if (dataAttributes[a] !== null) {
|
|
287
|
-
|
|
166
|
+
let attr = dataAttributes[a];
|
|
288
167
|
if (Array.isArray(attr) && attr.length === 1) {
|
|
289
168
|
;
|
|
290
|
-
|
|
169
|
+
[attr] = attr;
|
|
291
170
|
}
|
|
292
171
|
f[b] = attr;
|
|
293
172
|
}
|
|
@@ -296,7 +175,7 @@ var default_1 = /** @class */ (function (_super) {
|
|
|
296
175
|
// the SimpleFeature constructor takes care of recursively inflating subfeatures
|
|
297
176
|
if (data.child_features && data.child_features.length) {
|
|
298
177
|
f.subfeatures = data.child_features
|
|
299
|
-
.map(
|
|
178
|
+
.map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
|
|
300
179
|
.flat();
|
|
301
180
|
}
|
|
302
181
|
delete f.child_features;
|
|
@@ -306,9 +185,8 @@ var default_1 = /** @class */ (function (_super) {
|
|
|
306
185
|
delete f.attributes;
|
|
307
186
|
delete f.seq_id;
|
|
308
187
|
return f;
|
|
309
|
-
}
|
|
310
|
-
|
|
311
|
-
|
|
312
|
-
}(BaseAdapter_1.BaseFeatureDataAdapter));
|
|
188
|
+
}
|
|
189
|
+
freeResources( /* { region } */) { }
|
|
190
|
+
}
|
|
313
191
|
exports.default = default_1;
|
|
314
192
|
//# sourceMappingURL=Gff3TabixAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"Gff3TabixAdapter.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/Gff3TabixAdapter.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"Gff3TabixAdapter.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/Gff3TabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyC;AACzC,yEAGgD;AAChD,oDAAyD;AAEzD,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,uCAA8C;AAC9C,oDAAqE;AAErE,+DAGoC;AAWpC,eAAqB,SAAQ,oCAAsB;IAKjD,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,SAAS,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAChE,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC9D,MAAM,cAAc,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,CAAA;QAE/D,IAAI,CAAC,cAAc,GAAG,cAAc,IAAI,CAAC,YAAY,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAC1E,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;YAC3D,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,aAAa,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;SAChC,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YAC7C,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;QAC/D,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,iBAAiB,CAC7B,KAAa,EACb,OAAoB,EAAE,EACtB,QAA2D,EAC3D,QAA2B,EAC3B,eAAwB,EACxB,aAAa,GAAG,KAAK;QAErB,IAAI;YACF,MAAM,KAAK,GAAkB,EAAE,CAAA;YAE/B,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CACrB,KAAK,CAAC,OAAO,EACb,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,GAAG,EACT,CAAC,IAAY,EAAE,UAAkB,EAAE,EAAE;gBACnC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,aAAa,EAAE,IAAI,EAAE,UAAU,CAAC,CAAC,CAAA;YACtE,CAAC,CACF,CAAA;YACD,IAAI,eAAe,IAAI,KAAK,CAAC,MAAM,EAAE;gBACnC,IAAI,QAAQ,GAAG,QAAQ,CAAA;gBACvB,IAAI,MAAM,GAAG,CAAC,QAAQ,CAAA;gBACtB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACnB,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;oBAClC,yEAAyE;oBACzE,6CAA6C;oBAC7C,IAAI,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC9C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA,CAAC,iBAAiB;wBAC9C,IAAI,KAAK,GAAG,QAAQ,EAAE;4BACpB,QAAQ,GAAG,KAAK,CAAA;yBACjB;wBACD,IAAI,IAAI,CAAC,GAAG,GAAG,MAAM,EAAE;4BACrB,MAAM,GAAG,IAAI,CAAC,GAAG,CAAA;yBAClB;qBACF;gBACH,CAAC,CAAC,CAAA;gBACF,IAAI,MAAM,GAAG,KAAK,CAAC,GAAG,IAAI,QAAQ,GAAG,KAAK,CAAC,KAAK,EAAE;oBAChD,gEAAgE;oBAChE,8BAA8B;oBAC9B,IAAI,CAAC,iBAAiB,CACpB,EAAE,GAAG,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,EAAE,EAC1C,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,KAAK,CACN,CAAA;oBACD,OAAM;iBACP;aACF;YAED,MAAM,IAAI,GAAG,KAAK;iBACf,GAAG,CAAC,CAAC,UAAuB,EAAE,EAAE;gBAC/B,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBACxD,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC/C,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,cAAc,UAAU,CAAC,QAAQ,EAAE,CAAA;qBAC5D;iBACF;qBAAM;oBACL,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,aAAa,UAAU,CAAC,QAAQ,EAAE,CAAA;iBAC1D;gBACD,OAAO,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACrC,CAAC,CAAC;iBACD,IAAI,CAAC,IAAI,CAAC,CAAA;YAEb,MAAM,QAAQ,GAAG,aAAG,CAAC,eAAe,CAAC,IAAI,EAAE;gBACzC,aAAa,EAAE,IAAI;gBACnB,aAAa,EAAE,KAAK;gBACpB,eAAe,EAAE,KAAK;gBACtB,cAAc,EAAE,KAAK;aACtB,CAAC,CAAA;YAEF,QAAQ,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE,CAC7B,IAAI,CAAC,cAAc,CAAC,WAAW,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC3C,IACE,IAAA,sBAAc,EACZ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EACd,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EACZ,aAAa,CAAC,KAAK,EACnB,aAAa,CAAC,GAAG,CAClB,EACD;oBACA,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;iBACjB;YACH,CAAC,CAAC,CACH,CAAA;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;SACpB;QAAC,OAAO,CAAC,EAAE;YACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;SAClB;IACH,CAAC;IAEO,SAAS,CACf,aAA6C,EAC7C,IAAY,EACZ,UAAkB;QAElB,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE/B,yCAAyC;QACzC,OAAO;YACL,KAAK,EAAE,CAAC,MAAM,CAAC,aAAa,CAAC,KAAK,GAAG,CAAC,CAAC;YACvC,GAAG,EAAE,CAAC,MAAM,CAAC,aAAa,CAAC,GAAG,GAAG,CAAC,CAAC;YACnC,QAAQ,EAAE,UAAU;YACpB,MAAM;SACP,CAAA;IACH,CAAC;IAEO,cAAc,CAAC,WAAwB;QAC7C,OAAO,WAAW,CAAC,GAAG,CACpB,UAAU,CAAC,EAAE,CACX,IAAI,uBAAa,CAAC;YAChB,IAAI,EAAE,IAAI,CAAC,WAAW,CAAC,UAAU,CAAC;YAClC,oEAAoE;YACpE,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,WAAW,UAAU,CAAC,UAAW,CAAC,SAAU,CAAC,CAAC,CAAC,EAAE;SAChE,CAAC,CACL,CAAA;IACH,CAAC;IAEO,WAAW,CAAC,IAA6B;QAC/C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;QAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;QACjD,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YACvB,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SACd;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM;YACL,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;SACrB;QACD,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QACvB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,MAAM,aAAa,GAAG;YACpB,OAAO;YACP,KAAK;YACL,QAAQ;YACR,OAAO;YACP,MAAM;YACN,QAAQ;YACR,OAAO;YACP,QAAQ;SACT,CAAA;QACD,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAA;QAC5C,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACtC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;YACvB,IAAI,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE;gBAC7B,gDAAgD;gBAChD,gCAAgC;gBAChC,CAAC,IAAI,GAAG,CAAA;aACT;YACD,IAAI,cAAc,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;gBAC9B,IAAI,IAAI,GAAkC,cAAc,CAAC,CAAC,CAAC,CAAA;gBAC3D,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;oBAC5C,CAAC;oBAAA,CAAC,IAAI,CAAC,GAAG,IAAI,CAAA;iBACf;gBACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;aACZ;QACH,CAAC,CAAC,CAAA;QACF,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,CAAA;QAEpB,gFAAgF;QAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE;YACrD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc;iBAChC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;iBACvE,IAAI,EAAE,CAAA;SACV;QAED,OAAO,CAAC,CAAC,cAAc,CAAA;QACvB,OAAO,CAAC,CAAC,IAAI,CAAA;QACb,OAAO,CAAC,CAAC,gBAAgB,CAAA;QACzB,OAAO,CAAC,CAAC,SAAS,CAAA;QAClB,OAAO,CAAC,CAAC,UAAU,CAAA;QACnB,OAAO,CAAC,CAAC,MAAM,CAAA;QACf,OAAO,CAAC,CAAA;IACV,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAG,CAAC;CAC1C;AAtOD,4BAsOC"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
|
|
4
|
-
|
|
3
|
+
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
4
|
+
const configuration_1 = require("@jbrowse/core/configuration");
|
|
5
5
|
exports.default = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
|
|
6
6
|
gffGzLocation: {
|
|
7
7
|
type: 'fileLocation',
|
|
@@ -1 +1 @@
|
|
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1
|
-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,
|
|
1
|
+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,qDAAuC;AACvC,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,kBAAkB,EAClB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,KAAK,EAAE,IAAA,mCAAmB,EAAC,gBAAgB,EAAE;QAC3C,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF,cAAc,EAAE;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,CAAC,YAAY,EAAE,QAAQ,CAAC;KACvC;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
|
package/dist/index.js
CHANGED
|
@@ -1,19 +1,4 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __extends = (this && this.__extends) || (function () {
|
|
3
|
-
var extendStatics = function (d, b) {
|
|
4
|
-
extendStatics = Object.setPrototypeOf ||
|
|
5
|
-
({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
|
|
6
|
-
function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
|
|
7
|
-
return extendStatics(d, b);
|
|
8
|
-
};
|
|
9
|
-
return function (d, b) {
|
|
10
|
-
if (typeof b !== "function" && b !== null)
|
|
11
|
-
throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
|
|
12
|
-
extendStatics(d, b);
|
|
13
|
-
function __() { this.constructor = d; }
|
|
14
|
-
d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
|
|
15
|
-
};
|
|
16
|
-
})();
|
|
17
2
|
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
18
3
|
if (k2 === undefined) k2 = k;
|
|
19
4
|
var desc = Object.getOwnPropertyDescriptor(m, k);
|
|
@@ -41,34 +26,28 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
41
26
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
42
27
|
};
|
|
43
28
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
_this.name = 'GFF3Plugin';
|
|
54
|
-
return _this;
|
|
29
|
+
const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
|
|
30
|
+
const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
|
|
31
|
+
const Gff3TabixAdapter_1 = require("./Gff3TabixAdapter");
|
|
32
|
+
const tracks_1 = require("@jbrowse/core/util/tracks");
|
|
33
|
+
const Gff3Adapter_1 = require("./Gff3Adapter");
|
|
34
|
+
class default_1 extends Plugin_1.default {
|
|
35
|
+
constructor() {
|
|
36
|
+
super(...arguments);
|
|
37
|
+
this.name = 'GFF3Plugin';
|
|
55
38
|
}
|
|
56
|
-
|
|
57
|
-
pluginManager.addAdapterType(
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
var regexGuess = /\.gff3?\.b?gz$/i;
|
|
69
|
-
var adapterName = 'Gff3TabixAdapter';
|
|
70
|
-
var fileName = (0, tracks_1.getFileName)(file);
|
|
71
|
-
var indexName = index && (0, tracks_1.getFileName)(index);
|
|
39
|
+
install(pluginManager) {
|
|
40
|
+
pluginManager.addAdapterType(() => new AdapterType_1.default({
|
|
41
|
+
name: 'Gff3TabixAdapter',
|
|
42
|
+
configSchema: Gff3TabixAdapter_1.configSchema,
|
|
43
|
+
getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3TabixAdapter/Gff3TabixAdapter'))).then(r => r.default),
|
|
44
|
+
}));
|
|
45
|
+
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
46
|
+
return (file, index, adapterHint) => {
|
|
47
|
+
const regexGuess = /\.gff3?\.b?gz$/i;
|
|
48
|
+
const adapterName = 'Gff3TabixAdapter';
|
|
49
|
+
const fileName = (0, tracks_1.getFileName)(file);
|
|
50
|
+
const indexName = index && (0, tracks_1.getFileName)(index);
|
|
72
51
|
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
73
52
|
return {
|
|
74
53
|
type: adapterName,
|
|
@@ -83,21 +62,17 @@ var default_1 = /** @class */ (function (_super) {
|
|
|
83
62
|
return adapterGuesser(file, index, adapterHint);
|
|
84
63
|
};
|
|
85
64
|
});
|
|
86
|
-
pluginManager.addAdapterType(
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
var regexGuess = /\.gff3?$/i;
|
|
98
|
-
var adapterName = 'Gff3Adapter';
|
|
99
|
-
var fileName = (0, tracks_1.getFileName)(file);
|
|
100
|
-
var obj = {
|
|
65
|
+
pluginManager.addAdapterType(() => new AdapterType_1.default({
|
|
66
|
+
name: 'Gff3Adapter',
|
|
67
|
+
configSchema: Gff3Adapter_1.configSchema,
|
|
68
|
+
getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3Adapter/Gff3Adapter'))).then(r => r.default),
|
|
69
|
+
}));
|
|
70
|
+
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
71
|
+
return (file, index, adapterHint) => {
|
|
72
|
+
const regexGuess = /\.gff3?$/i;
|
|
73
|
+
const adapterName = 'Gff3Adapter';
|
|
74
|
+
const fileName = (0, tracks_1.getFileName)(file);
|
|
75
|
+
const obj = {
|
|
101
76
|
type: adapterName,
|
|
102
77
|
gffLocation: file,
|
|
103
78
|
};
|
|
@@ -110,8 +85,7 @@ var default_1 = /** @class */ (function (_super) {
|
|
|
110
85
|
return adapterGuesser(file, index, adapterHint);
|
|
111
86
|
};
|
|
112
87
|
});
|
|
113
|
-
}
|
|
114
|
-
|
|
115
|
-
}(Plugin_1.default));
|
|
88
|
+
}
|
|
89
|
+
}
|
|
116
90
|
exports.default = default_1;
|
|
117
91
|
//# sourceMappingURL=index.js.map
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kGAAyE;AAEzE,kEAAyC;AACzC,yDAAiF;AAEjF,sDAKkC;AAClC,+CAAuE;AAEvE,eAAqB,SAAQ,gBAAM;IAAnC;;QACE,SAAI,GAAG,YAAY,CAAA;IAyErB,CAAC;IAvEC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,kBAAkB;YACxB,YAAY,EAAE,+BAA4B;YAC1C,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,qCAAqC,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACrE,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,kBAAkB,CAAA;gBACtC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,IAAA,oBAAW,EAAC,KAAK,CAAC,CAAA;gBAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,WAAW,EAAE,IAAI;wBACjB,aAAa,EAAE,IAAI;wBACnB,KAAK,EAAE;4BACL,QAAQ,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,MAAM,CAAC;4BAC1C,SAAS,EAAE,IAAA,sBAAa,EAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;yBAClD;qBACF,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;YACd,IAAI,EAAE,aAAa;YACnB,YAAY,EAAE,0BAAuB;YACrC,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,2BAA2B,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SAC3D,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,WAAW,CAAA;gBAC9B,MAAM,WAAW,GAAG,aAAa,CAAA;gBACjC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;iBAClB,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;CACF;AA1ED,4BA0EC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-gff3",
|
|
3
|
-
"version": "2.1.
|
|
3
|
+
"version": "2.1.2",
|
|
4
4
|
"description": "JBrowse 2 gff3.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -37,7 +37,6 @@
|
|
|
37
37
|
"clean": "rimraf dist esm *.tsbuildinfo"
|
|
38
38
|
},
|
|
39
39
|
"dependencies": {
|
|
40
|
-
"@babel/runtime": "^7.17.9",
|
|
41
40
|
"@flatten-js/interval-tree": "^1.0.15",
|
|
42
41
|
"@gmod/bgzf-filehandle": "^1.4.3",
|
|
43
42
|
"@gmod/gff": "^1.2.0",
|
|
@@ -60,5 +59,5 @@
|
|
|
60
59
|
"distModule": "esm/index.js",
|
|
61
60
|
"srcModule": "src/index.ts",
|
|
62
61
|
"module": "esm/index.js",
|
|
63
|
-
"gitHead": "
|
|
62
|
+
"gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
|
|
64
63
|
}
|