@jbrowse/plugin-bed 2.1.0 → 2.1.2

package/dist/BedAdapter/BedAdapter.js

@@ -1,273 +1,136 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            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;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var bed_1 = __importDefault(require("@gmod/bed"));
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var io_1 = require("@jbrowse/core/util/io");
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var util_1 = require("../util");
-var interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+const bed_1 = __importDefault(require("@gmod/bed"));
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const util_1 = require("../util");
+const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 function isGzip(buf) {
     return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-var BedAdapter = /** @class */ (function (_super) {
-    __extends(BedAdapter, _super);
-    function BedAdapter() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.intervalTrees = {};
-        return _this;
+class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.intervalTrees = {};
     }
-    BedAdapter.prototype.loadDataP = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var pm, bedLoc, buf, buffer, _a, data, lines, headerLines, i, header, features, line, tab, refName, autoSql, parser, columnNames, scoreColumn, colRef, colStart, colEnd;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        pm = this.pluginManager;
-                        bedLoc = this.getConf('bedLocation');
-                        return [4 /*yield*/, (0, io_1.openLocation)(bedLoc, pm).readFile(opts)];
-                    case 1:
-                        buf = _b.sent();
-                        if (!isGzip(buf)) return [3 /*break*/, 3];
-                        return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buf)];
-                    case 2:
-                        _a = _b.sent();
-                        return [3 /*break*/, 4];
-                    case 3:
-                        _a = buf;
-                        _b.label = 4;
-                    case 4:
-                        buffer = _a;
-                        // 512MB  max chrome string length is 512MB
-                        if (buffer.length > 536870888) {
-                            throw new Error('Data exceeds maximum string length (512MB)');
-                        }
-                        data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
-                        lines = data.split('\n').filter(function (f) { return !!f; });
-                        headerLines = [];
-                        i = 0;
-                        for (; i < lines.length && lines[i].startsWith('#'); i++) {
-                            headerLines.push(lines[i]);
-                        }
-                        header = headerLines.join('\n');
-                        features = {};
-                        for (; i < lines.length; i++) {
-                            line = lines[i];
-                            tab = line.indexOf('\t');
-                            refName = line.slice(0, tab);
-                            if (!features[refName]) {
-                                features[refName] = [];
-                            }
-                            features[refName].push(line);
-                        }
-                        autoSql = this.getConf('autoSql');
-                        parser = new bed_1.default({ autoSql: autoSql });
-                        columnNames = this.getConf('columnNames');
-                        scoreColumn = this.getConf('scoreColumn');
-                        colRef = this.getConf('colRef');
-                        colStart = this.getConf('colStart');
-                        colEnd = this.getConf('colEnd');
-                        return [2 /*return*/, {
-                                header: header,
-                                features: features,
-                                parser: parser,
-                                columnNames: columnNames,
-                                scoreColumn: scoreColumn,
-                                colRef: colRef,
-                                colStart: colStart,
-                                colEnd: colEnd,
-                            }];
-                }
-            });
-        });
-    };
-    BedAdapter.prototype.loadData = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (!this.bedFeatures) {
-                    this.bedFeatures = this.loadDataP(opts).catch(function (e) {
-                        _this.bedFeatures = undefined;
-                        throw e;
-                    });
-                }
-                return [2 /*return*/, this.bedFeatures];
-            });
-        });
-    };
-    BedAdapter.prototype.getRefNames = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var features;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.loadData(opts)];
-                    case 1:
-                        features = (_a.sent()).features;
-                        return [2 /*return*/, Object.keys(features)];
-                }
-            });
-        });
-    };
-    BedAdapter.prototype.getHeader = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var header;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.loadData(opts)];
-                    case 1:
-                        header = (_a.sent()).header;
-                        return [2 /*return*/, header];
-                }
-            });
-        });
-    };
-    BedAdapter.prototype.getNames = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var _a, header, columnNames, defs, defline;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0: return [4 /*yield*/, this.loadData()];
-                    case 1:
-                        _a = _b.sent(), header = _a.header, columnNames = _a.columnNames;
-                        if (columnNames.length) {
-                            return [2 /*return*/, columnNames];
-                        }
-                        defs = header.split('\n').filter(function (f) { return !!f; });
-                        defline = defs[defs.length - 1];
-                        return [2 /*return*/, (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
-                                ? defline
-                                    .slice(1)
-                                    .split('\t')
-                                    .map(function (field) { return field.trim(); })
-                                : undefined];
-                }
-            });
-        });
-    };
-    BedAdapter.prototype.loadFeatureIntervalTreeHelper = function (refName) {
-        return __awaiter(this, void 0, void 0, function () {
-            var _a, colRef, colStart, colEnd, features, parser, scoreColumn, lines, names, intervalTree, ret, i, obj;
-            var _this = this;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0: return [4 /*yield*/, this.loadData()];
-                    case 1:
-                        _a = _b.sent(), colRef = _a.colRef, colStart = _a.colStart, colEnd = _a.colEnd, features = _a.features, parser = _a.parser, scoreColumn = _a.scoreColumn;
-                        lines = features[refName];
-                        if (!lines) {
-                            return [2 /*return*/, undefined];
-                        }
-                        return [4 /*yield*/, this.getNames()];
-                    case 2:
-                        names = _b.sent();
-                        intervalTree = new interval_tree_1.default();
-                        ret = lines.map(function (f, i) {
-                            var uniqueId = "".concat(_this.id, "-").concat(refName, "-").concat(i);
-                            return (0, util_1.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
-                        });
-                        for (i = 0; i < ret.length; i++) {
-                            obj = ret[i];
-                            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
-                        }
-                        return [2 /*return*/, intervalTree];
-                }
-            });
-        });
-    };
-    BedAdapter.prototype.loadFeatureIntervalTree = function (refName) {
-        return __awaiter(this, void 0, void 0, function () {
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (!this.intervalTrees[refName]) {
-                    this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(function (e) {
-                        _this.intervalTrees[refName] = undefined;
-                        throw e;
-                    });
-                }
-                return [2 /*return*/, this.intervalTrees[refName]];
+    async loadDataP(opts = {}) {
+        const pm = this.pluginManager;
+        const bedLoc = this.getConf('bedLocation');
+        const buf = await (0, io_1.openLocation)(bedLoc, pm).readFile(opts);
+        const buffer = isGzip(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
+        // 512MB  max chrome string length is 512MB
+        if (buffer.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const lines = data.split('\n').filter(f => !!f);
+        const headerLines = [];
+        let i = 0;
+        for (; i < lines.length && lines[i].startsWith('#'); i++) {
+            headerLines.push(lines[i]);
+        }
+        const header = headerLines.join('\n');
+        const features = {};
+        for (; i < lines.length; i++) {
+            const line = lines[i];
+            const tab = line.indexOf('\t');
+            const refName = line.slice(0, tab);
+            if (!features[refName]) {
+                features[refName] = [];
+            }
+            features[refName].push(line);
+        }
+        const autoSql = this.getConf('autoSql');
+        const parser = new bed_1.default({ autoSql });
+        const columnNames = this.getConf('columnNames');
+        const scoreColumn = this.getConf('scoreColumn');
+        const colRef = this.getConf('colRef');
+        const colStart = this.getConf('colStart');
+        const colEnd = this.getConf('colEnd');
+        return {
+            header,
+            features,
+            parser,
+            columnNames,
+            scoreColumn,
+            colRef,
+            colStart,
+            colEnd,
+        };
+    }
+    async loadData(opts = {}) {
+        if (!this.bedFeatures) {
+            this.bedFeatures = this.loadDataP(opts).catch(e => {
+                this.bedFeatures = undefined;
+                throw e;
             });
+        }
+        return this.bedFeatures;
+    }
+    async getRefNames(opts = {}) {
+        const { features } = await this.loadData(opts);
+        return Object.keys(features);
+    }
+    async getHeader(opts = {}) {
+        const { header } = await this.loadData(opts);
+        return header;
+    }
+    async getNames() {
+        const { header, columnNames } = await this.loadData();
+        if (columnNames.length) {
+            return columnNames;
+        }
+        const defs = header.split('\n').filter(f => !!f);
+        const defline = defs[defs.length - 1];
+        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+            ? defline
+                .slice(1)
+                .split('\t')
+                .map(field => field.trim())
+            : undefined;
+    }
+    async loadFeatureIntervalTreeHelper(refName) {
+        const { colRef, colStart, colEnd, features, parser, scoreColumn } = await this.loadData();
+        const lines = features[refName];
+        if (!lines) {
+            return undefined;
+        }
+        const names = await this.getNames();
+        const intervalTree = new interval_tree_1.default();
+        const ret = lines.map((f, i) => {
+            const uniqueId = `${this.id}-${refName}-${i}`;
+            return (0, util_1.featureData)(f, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names);
         });
-    };
-    BedAdapter.prototype.getFeatures = function (query, opts) {
-        var _this = this;
-        if (opts === void 0) { opts = {}; }
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var start, end, refName, intervalTree;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        start = query.start, end = query.end, refName = query.refName;
-                        return [4 /*yield*/, this.loadFeatureIntervalTree(refName)];
-                    case 1:
-                        intervalTree = _a.sent();
-                        intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(function (f) { return observer.next(f); });
-                        observer.complete();
-                        return [2 /*return*/];
-                }
+        for (let i = 0; i < ret.length; i++) {
+            const obj = ret[i];
+            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+        }
+        return intervalTree;
+    }
+    async loadFeatureIntervalTree(refName) {
+        if (!this.intervalTrees[refName]) {
+            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(e => {
+                this.intervalTrees[refName] = undefined;
+                throw e;
             });
-        }); }, opts.signal);
-    };
-    BedAdapter.prototype.freeResources = function () { };
-    BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
-    return BedAdapter;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+        }
+        return this.intervalTrees[refName];
+    }
+    getFeatures(query, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { start, end, refName } = query;
+            const intervalTree = await this.loadFeatureIntervalTree(refName);
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => observer.next(f));
+            observer.complete();
+        }, opts.signal);
+    }
+    freeResources() { }
+}
 exports.default = BedAdapter;
+BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 //# sourceMappingURL=BedAdapter.js.map

package/dist/BedAdapter/BedAdapter.js.map

@@ -1 +1 @@
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package/dist/BedAdapter/configSchema.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
+const configuration_1 = require("@jbrowse/core/configuration");
 exports.default = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
     bedLocation: {
         type: 'fileLocation',

package/dist/BedAdapter/configSchema.js.map

@@ -1 +1 @@
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