@jbrowse/plugin-bed 1.7.9 → 2.0.0

package/dist/BedAdapter/BedAdapter.d.ts

@@ -0,0 +1,29 @@
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import IntervalTree from '@flatten-js/interval-tree';
+export default class BedAdapter extends BaseFeatureDataAdapter {
+    protected bedFeatures?: Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        parser: typeof BED;
+        columnNames: string[];
+        scoreColumn: string;
+        colRef: number;
+        colStart: number;
+        colEnd: number;
+    }>;
+    protected intervalTrees: {
+        [key: string]: Promise<IntervalTree | undefined> | undefined;
+    };
+    static capabilities: string[];
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<string>;
+    getNames(): Promise<string[] | undefined>;
+    private loadFeatureIntervalTreeHelper;
+    private loadFeatureIntervalTree;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/BedAdapter/BedAdapter.js

@@ -0,0 +1,273 @@
+"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");
+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;
+    }
+    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]];
+            });
+        });
+    };
+    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*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    BedAdapter.prototype.freeResources = function () { };
+    BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
+    return BedAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = BedAdapter;
+//# sourceMappingURL=BedAdapter.js.map

package/dist/BedAdapter/BedAdapter.js.map

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package/dist/BedAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/BedAdapter/configSchema.js

@@ -0,0 +1,40 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
+    bedLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+    scoreColumn: {
+        type: 'string',
+        description: 'The column to use as a "score" attribute',
+        defaultValue: '',
+    },
+    autoSql: {
+        type: 'string',
+        description: 'The autoSql definition for the data fields in the file',
+        defaultValue: '',
+    },
+    colRef: {
+        type: 'number',
+        description: 'The column to use as a "refName" attribute',
+        defaultValue: 0,
+    },
+    colStart: {
+        type: 'number',
+        description: 'The column to use as a "start" attribute',
+        defaultValue: 1,
+    },
+    colEnd: {
+        type: 'number',
+        description: 'The column to use as a "end" attribute',
+        defaultValue: 2,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/BedAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,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;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4CAA4C;QACzD,YAAY,EAAE,CAAC;KAChB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,CAAC;KAChB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wCAAwC;QACrD,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/BedAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/dist/BedAdapter/index.js

@@ -0,0 +1,9 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/BedAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BedAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -1,9 +1,8 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Region, Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     private parser;
@@ -14,10 +13,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<any>;
     getHeader(): Promise<string>;
-    defaultParser(fields: string[], line: string): {
-        [k: string]: string;
-    };
-    getNames(): Promise<string[] | null>;
+    getNames(): Promise<string[] | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }