@jbrowse/plugin-bed 2.1.0 → 2.1.3
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/BedAdapter/BedAdapter.js +122 -259
- package/dist/BedAdapter/BedAdapter.js.map +1 -1
- package/dist/BedAdapter/configSchema.js +1 -1
- package/dist/BedAdapter/configSchema.js.map +1 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.js +61 -146
- package/dist/BedTabixAdapter/BedTabixAdapter.js.map +1 -1
- package/dist/BedTabixAdapter/configSchema.js +2 -2
- package/dist/BedTabixAdapter/configSchema.js.map +1 -1
- package/dist/BigBedAdapter/BigBedAdapter.js +95 -219
- package/dist/BigBedAdapter/BigBedAdapter.js.map +1 -1
- package/dist/BigBedAdapter/configSchema.js +1 -1
- package/dist/BigBedAdapter/configSchema.js.map +1 -1
- package/dist/index.js +45 -75
- package/dist/index.js.map +1 -1
- package/dist/util.js +62 -67
- package/dist/util.js.map +1 -1
- package/package.json +2 -3
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"use strict";
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var __extends = (this && this.__extends) || (function () {
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var extendStatics = function (d, b) {
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extendStatics = Object.setPrototypeOf ||
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({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
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function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
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throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
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function __() { this.constructor = d; }
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d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
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var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
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function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
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return new (P || (P = Promise))(function (resolve, reject) {
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function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
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function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
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function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
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var __generator = (this && this.__generator) || function (thisArg, body) {
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return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
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function verb(n) { return function (v) { return step([n, v]); }; }
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if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
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if (y = 0, t) op = [op[0] & 2, t.value];
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case 0: case 1: t = op; break;
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case 4: _.label++; return { value: op[1], done: false };
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case 5: _.label++; y = op[1]; op = [0]; continue;
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case 7: op = _.ops.pop(); _.trys.pop(); continue;
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if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
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if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
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if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
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}
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} catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
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if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
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};
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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_this.bed = new tabix_1.TabixIndexedFile({
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const bed_1 = __importDefault(require("@gmod/bed"));
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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 tabix_1 = require("@gmod/tabix");
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const util_1 = require("../util");
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class BedTabixAdapter 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 bedGzLoc = this.getConf('bedGzLocation');
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const type = this.getConf(['index', 'indexType']);
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const loc = this.getConf(['index', 'location']);
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const autoSql = this.getConf('autoSql');
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const pm = this.pluginManager;
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this.bed = new tabix_1.TabixIndexedFile({
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filehandle: (0, io_1.openLocation)(bedGzLoc, pm),
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csiFilehandle: type === 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
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tbiFilehandle: type !== 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
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chunkCacheSize: 50 *
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chunkCacheSize: 50 * 2 ** 20,
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});
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return _this;
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this.columnNames = this.getConf('columnNames');
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this.scoreColumn = this.getConf('scoreColumn');
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this.parser = new bed_1.default({ autoSql });
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}
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});
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});
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};
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BedTabixAdapter.prototype.getFeatures = function (query, opts) {
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var _this = this;
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if (opts === void 0) { opts = {}; }
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return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
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var meta, columnNumbers, colRef, colStart, colEnd, names;
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var _this = this;
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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.bed.getMetadata()];
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case 1:
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meta = _a.sent();
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columnNumbers = meta.columnNumbers;
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colRef = columnNumbers.ref - 1;
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colStart = columnNumbers.start - 1;
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colEnd = columnNumbers.end - 1;
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return [4 /*yield*/, this.getNames()];
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case 2:
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names = _a.sent();
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return [4 /*yield*/, this.bed.getLines(query.refName, query.start, query.end, {
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lineCallback: function (line, fileOffset) {
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observer.next((0, util_1.featureData)(line, colRef, colStart, colEnd, _this.scoreColumn, _this.parser, "".concat(_this.id, "-").concat(fileOffset), names));
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},
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signal: opts.signal,
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})];
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case 3:
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_a.sent();
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observer.complete();
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return [2 /*return*/];
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}
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async getRefNames(opts = {}) {
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return this.bed.getReferenceSequenceNames(opts);
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}
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async getHeader() {
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return this.bed.getHeader();
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}
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async getNames() {
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if (this.columnNames.length) {
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return this.columnNames;
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}
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const header = await this.bed.getHeader();
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const defs = header.split('\n').filter(f => !!f);
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const defline = defs[defs.length - 1];
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return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
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? defline
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.slice(1)
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.split('\t')
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.map(f => f.trim())
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: undefined;
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}
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getFeatures(query, opts = {}) {
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return (0, rxjs_1.ObservableCreate)(async (observer) => {
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const meta = await this.bed.getMetadata();
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const { columnNumbers } = meta;
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const colRef = columnNumbers.ref - 1;
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const colStart = columnNumbers.start - 1;
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const colEnd = columnNumbers.end - 1;
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// colSame handles special case for tabix where a single column is both
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// the start and end, this is assumed to be covering the base at this
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// position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same
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const names = await this.getNames();
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await this.bed.getLines(query.refName, query.start, query.end, {
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lineCallback: (line, fileOffset) => {
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observer.next((0, util_1.featureData)(line, colRef, colStart, colEnd, this.scoreColumn, this.parser, `${this.id}-${fileOffset}`, names));
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},
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signal: opts.signal,
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});
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}(BaseAdapter_1.BaseFeatureDataAdapter));
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observer.complete();
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}, opts.signal);
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}
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freeResources() { }
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}
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exports.default = BedTabixAdapter;
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BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
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//# sourceMappingURL=BedTabixAdapter.js.map
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{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":"
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{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,kCAAqC;AAKrC,MAAqB,eAAgB,SAAQ,oCAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAChD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YACvB,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YACzC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;YAC9B,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,MAAM,QAAQ,GAAG,aAAa,CAAC,KAAK,GAAG,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,uEAAuE;YACvE,qEAAqE;YACrE,8DAA8D;YAC9D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YACnC,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE;gBAC7D,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAA,kBAAW,EACT,IAAI,EACJ,MAAM,EACN,QAAQ,EACR,MAAM,EACN,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,MAAM,EACX,GAAG,IAAI,CAAC,EAAE,IAAI,UAAU,EAAE,EAC1B,KAAK,CACN,CACF,CAAA;gBACH,CAAC;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzFjC,kCA0FC;AAjFe,4BAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC,kBAAe,IAAA,mCAAmB,EAChC,iBAAiB,EACjB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,KAAK,EAAE,IAAA,mCAAmB,EAAC,YAAY,EAAE;QACvC,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;IAEF,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
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async getHeader(opts) {
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|
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|
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|
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|
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};
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}
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
+
const data = parser.parseLine(`${refName}\t${r.start}\t${r.end}\t${r.rest}`, {
|
|
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+
uniqueId: r.uniqueId,
|
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65
|
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return __awaiter(this, void 0, void 0, function () {
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_a = _c.sent(), parser = _a.parser, header = _a.header;
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version = header.version, fileType = header.fileType;
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_b = parser.autoSql, fields = _b.fields, rest = __rest(_b, ["fields"]);
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BigBedAdapter.prototype.getFeatures = function (region, opts) {
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if (opts === void 0) { opts = {}; }
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var refName = region.refName, start = region.start, end = region.end;
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var _this = this;
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_b.trys.push([0, 3, , 4]);
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return [4 /*yield*/, this.configure(opts)];
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case 1:
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_a = _b.sent(), parser_1 = _a.parser, bigbed = _a.bigbed;
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return [4 /*yield*/, bigbed.getFeatureStream(refName, start, end, {
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signal: signal,
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})];
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case 2:
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ob = _b.sent();
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|
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ob.pipe((0, operators_1.mergeAll)(), (0, operators_1.map)(function (r) {
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|
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var data = parser_1.parseLine("".concat(refName, "\t").concat(r.start, "\t").concat(r.end, "\t").concat(r.rest), {
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|
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uniqueId: r.uniqueId,
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});
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|
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var blockCount = data.blockCount, blockSizes = data.blockSizes, blockStarts = data.blockStarts, chromStarts = data.chromStarts;
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|
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|
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|
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var starts = chromStarts || blockStarts || [];
|
|
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|
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|
|
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|
-
var blocksOffset = r.start;
|
|
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|
-
data.subfeatures = [];
|
|
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|
-
for (var b = 0; b < blockCount; b += 1) {
|
|
197
|
-
var bmin = (starts[b] || 0) + blocksOffset;
|
|
198
|
-
var bmax = bmin + (sizes[b] || 0);
|
|
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|
-
data.subfeatures.push({
|
|
200
|
-
uniqueId: "".concat(r.uniqueId, "-").concat(b),
|
|
201
|
-
start: bmin,
|
|
202
|
-
end: bmax,
|
|
203
|
-
type: 'block',
|
|
204
|
-
});
|
|
205
|
-
}
|
|
206
|
-
}
|
|
207
|
-
if (r.uniqueId === undefined) {
|
|
208
|
-
throw new Error('invalid bbi feature');
|
|
209
|
-
}
|
|
210
|
-
var chromStart = data.chromStart, chromEnd = data.chromEnd, chrom = data.chrom, rest = __rest(data, ["chromStart", "chromEnd", "chrom"]);
|
|
211
|
-
var f = new simpleFeature_1.default({
|
|
212
|
-
id: "".concat(_this.id, "-").concat(r.uniqueId),
|
|
213
|
-
data: __assign(__assign({}, rest), { start: r.start, end: r.end, refName: refName }),
|
|
66
|
+
const { blockCount, blockSizes, blockStarts, chromStarts } = data;
|
|
67
|
+
if (blockCount) {
|
|
68
|
+
const starts = chromStarts || blockStarts || [];
|
|
69
|
+
const sizes = blockSizes;
|
|
70
|
+
const blocksOffset = r.start;
|
|
71
|
+
data.subfeatures = [];
|
|
72
|
+
for (let b = 0; b < blockCount; b += 1) {
|
|
73
|
+
const bmin = (starts[b] || 0) + blocksOffset;
|
|
74
|
+
const bmax = bmin + (sizes[b] || 0);
|
|
75
|
+
data.subfeatures.push({
|
|
76
|
+
uniqueId: `${r.uniqueId}-${b}`,
|
|
77
|
+
start: bmin,
|
|
78
|
+
end: bmax,
|
|
79
|
+
type: 'block',
|
|
214
80
|
});
|
|
215
|
-
|
|
216
|
-
|
|
217
|
-
|
|
218
|
-
|
|
219
|
-
|
|
220
|
-
|
|
221
|
-
|
|
222
|
-
|
|
223
|
-
|
|
224
|
-
|
|
225
|
-
|
|
226
|
-
|
|
227
|
-
|
|
228
|
-
|
|
229
|
-
|
|
230
|
-
|
|
231
|
-
|
|
232
|
-
|
|
81
|
+
}
|
|
82
|
+
}
|
|
83
|
+
if (r.uniqueId === undefined) {
|
|
84
|
+
throw new Error('invalid bbi feature');
|
|
85
|
+
}
|
|
86
|
+
const { chromStart, chromEnd, chrom, ...rest } = data;
|
|
87
|
+
const f = new simpleFeature_1.default({
|
|
88
|
+
id: `${this.id}-${r.uniqueId}`,
|
|
89
|
+
data: {
|
|
90
|
+
...rest,
|
|
91
|
+
start: r.start,
|
|
92
|
+
end: r.end,
|
|
93
|
+
refName,
|
|
94
|
+
},
|
|
95
|
+
});
|
|
96
|
+
// collection of heuristics for suggesting that this feature
|
|
97
|
+
// should be converted to a gene, CNV bigbed has many gene like
|
|
98
|
+
// features including thickStart and blockCount but no strand
|
|
99
|
+
return isUCSC(f) ? (0, util_1.ucscProcessedTranscript)(f) : f;
|
|
100
|
+
})).subscribe(observer);
|
|
101
|
+
}
|
|
102
|
+
catch (e) {
|
|
103
|
+
observer.error(e);
|
|
104
|
+
}
|
|
105
|
+
}, opts.signal);
|
|
106
|
+
}
|
|
107
|
+
freeResources() { }
|
|
108
|
+
}
|
|
233
109
|
exports.default = BigBedAdapter;
|
|
234
110
|
//# sourceMappingURL=BigBedAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BigBedAdapter.js","sourceRoot":"","sources":["../../src/BigBedAdapter/BigBedAdapter.ts"],"names":[],"mappings":"
|
|
1
|
+
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|