@jbrowse/plugin-bed 3.7.0 → 4.0.0

package/dist/BedAdapter/BedAdapter.d.ts

@@ -1,36 +0,0 @@
-import { IntervalTree } from '@flatten-js/interval-tree';
-import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature, Region } from '@jbrowse/core/util';
-export default class BedAdapter extends BaseFeatureDataAdapter {
-    protected bedFeatures?: Promise<{
-        header: string;
-        features: Record<string, string[]>;
-        parser: BED;
-        columnNames: string[];
-        scoreColumn: string;
-        colRef: number;
-        colStart: number;
-        colEnd: number;
-    }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
-    static capabilities: string[];
-    private loadDataP;
-    loadData(opts?: BaseOptions): Promise<{
-        header: string;
-        features: Record<string, string[]>;
-        parser: BED;
-        columnNames: string[];
-        scoreColumn: string;
-        colRef: number;
-        colStart: number;
-        colEnd: number;
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getNames(): Promise<string[] | undefined>;
-    private loadFeatureIntervalTreeHelper;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}

package/dist/BedAdapter/BedAdapter.js

@@ -1,137 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const interval_tree_1 = require("@flatten-js/interval-tree");
-const bed_1 = __importDefault(require("@gmod/bed"));
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_2 = require("../util");
-class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.intervalTrees = {};
-    }
-    async loadDataP(opts) {
-        const bedLoc = this.getConf('bedLocation');
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, this.pluginManager), opts);
-        const headerLines = [];
-        const features = {};
-        (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
-            if (line.startsWith('#')) {
-                headerLines.push(line);
-            }
-            else {
-                const tab = line.indexOf('\t');
-                const refName = line.slice(0, tab);
-                if (!features[refName]) {
-                    features[refName] = [];
-                }
-                features[refName].push(line);
-            }
-            return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
-        const header = headerLines.join('\n');
-        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|\r\n|\r/).filter(f => !!f);
-        const defline = defs.at(-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.IntervalTree();
-        for (let i = 0; i < lines.length; i++) {
-            const line = lines[i];
-            const uniqueId = `${this.id}-${refName}-${i}`;
-            const feat = new util_1.SimpleFeature((0, util_2.featureData)({
-                line,
-                colRef,
-                colStart,
-                colEnd,
-                scoreColumn,
-                parser,
-                uniqueId,
-                names,
-            }));
-            intervalTree.insert([feat.get('start'), feat.get('end')], feat);
-        }
-        return intervalTree;
-    }
-    async loadFeatureIntervalTree(refName) {
-        if (!this.intervalTrees[refName]) {
-            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch((e) => {
-                this.intervalTrees[refName] = undefined;
-                throw e;
-            });
-        }
-        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);
-            const features = intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]);
-            if (features) {
-                for (const f of features) {
-                    observer.next(f);
-                }
-            }
-            observer.complete();
-        }, opts.stopToken);
-    }
-}
-BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = BedAdapter;

package/dist/BedAdapter/configSchema.d.ts

@@ -1,41 +0,0 @@
-declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    bedLocation: {
-        type: string;
-        description: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    columnNames: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-    scoreColumn: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    autoSql: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    colRef: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    colStart: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    colEnd: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BedAdapter;

package/dist/BedAdapter/configSchema.js

@@ -1,58 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
-    bedLocation: {
-        type: 'fileLocation',
-        description: 'path to bed file, also allows gzipped bed',
-        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,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                bedLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = BedAdapter;

package/dist/BedAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function BedAdapterF(pluginManager: PluginManager): void;

package/dist/BedAdapter/index.js

@@ -1,49 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = BedAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BedAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'BedAdapter',
-        displayName: 'BED adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedAdapter'))).then(r => r.default),
-    }));
-}

package/dist/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -1,23 +0,0 @@
-import { IntervalTree } from '@flatten-js/interval-tree';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature, Region } from '@jbrowse/core/util';
-export default class BedGraphAdapter extends BaseFeatureDataAdapter {
-    protected bedFeatures?: Promise<{
-        header: string;
-        features: Record<string, string[]>;
-        columnNames: string[];
-    }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
-    getNames(): Promise<string[] | undefined>;
-    private loadFeatureIntervalTreeHelper;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    private loadDataP;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
-    loadData(opts?: BaseOptions): Promise<{
-        header: string;
-        features: Record<string, string[]>;
-        columnNames: string[];
-    }>;
-    getFeatures(query: Region, _opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}

package/dist/BedGraphAdapter/BedGraphAdapter.js

@@ -1,122 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const interval_tree_1 = require("@flatten-js/interval-tree");
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.intervalTrees = {};
-    }
-    async getNames() {
-        const { header, columnNames } = await this.loadData();
-        if (columnNames.length) {
-            return columnNames;
-        }
-        const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
-        const defline = defs.at(-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) {
-        var _a;
-        const { features } = await this.loadData();
-        const lines = features[refName];
-        if (!lines) {
-            return undefined;
-        }
-        const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(3)) || [];
-        const intervalTree = new interval_tree_1.IntervalTree();
-        for (let i = 0, l = lines.length; i < l; i++) {
-            const line = lines[i];
-            const [refName, s, e, ...rest] = line.split('\t');
-            for (let j = 0, l2 = rest.length; j < l2; j++) {
-                const uniqueId = `${this.id}-${refName}-${i}-${j}`;
-                const start = +s;
-                const end = +e;
-                const score = +rest[j];
-                const source = names[j] || `col${j}`;
-                if (score) {
-                    intervalTree.insert([start, end], new util_1.SimpleFeature({
-                        id: uniqueId,
-                        data: {
-                            refName,
-                            start,
-                            end,
-                            score,
-                            source,
-                        },
-                    }));
-                }
-            }
-        }
-        return intervalTree;
-    }
-    async getRefNames(opts = {}) {
-        const { features } = await this.loadData(opts);
-        return Object.keys(features);
-    }
-    async loadDataP(opts = {}) {
-        const pm = this.pluginManager;
-        const bedLoc = this.getConf('bedGraphLocation');
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(bedLoc, pm), opts);
-        const features = {};
-        const headerLines = [];
-        (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
-            if (line.startsWith('#')) {
-                headerLines.push(line);
-            }
-            else {
-                const tab = line.indexOf('\t');
-                const refName = line.slice(0, tab);
-                if (!features[refName]) {
-                    features[refName] = [];
-                }
-                features[refName].push(line);
-            }
-            return true;
-        }, opts.statusCallback);
-        const columnNames = this.getConf('columnNames');
-        return {
-            header: headerLines.join('\n'),
-            features,
-            columnNames,
-        };
-    }
-    async loadFeatureIntervalTree(refName) {
-        if (!this.intervalTrees[refName]) {
-            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch((e) => {
-                this.intervalTrees[refName] = undefined;
-                throw e;
-            });
-        }
-        return this.intervalTrees[refName];
-    }
-    async loadData(opts = {}) {
-        if (!this.bedFeatures) {
-            this.bedFeatures = this.loadDataP(opts).catch((e) => {
-                this.bedFeatures = undefined;
-                throw e;
-            });
-        }
-        return this.bedFeatures;
-    }
-    getFeatures(query, _opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { start, end, refName } = query;
-            const intervalTree = await this.loadFeatureIntervalTree(refName);
-            for (const feature of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
-                observer.next(feature);
-            }
-            observer.complete();
-        });
-    }
-}
-exports.default = BedGraphAdapter;

package/dist/BedGraphAdapter/configSchema.d.ts

@@ -1,15 +0,0 @@
-declare const BedGraphAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    bedGraphLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    columnNames: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BedGraphAdapter;

package/dist/BedGraphAdapter/configSchema.js

@@ -1,32 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const BedGraphAdapter = (0, configuration_1.ConfigurationSchema)('BedGraphAdapter', {
-    bedGraphLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.bedgraph',
-            locationType: 'UriLocation',
-        },
-    },
-    columnNames: {
-        type: 'stringArray',
-        description: 'List of column names',
-        defaultValue: [],
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                bedGraphLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = BedGraphAdapter;

package/dist/BedGraphAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function BedGraphAdapterF(pluginManager: PluginManager): void;

package/dist/BedGraphAdapter/index.js

@@ -1,49 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = BedGraphAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BedGraphAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'BedGraphAdapter',
-        displayName: 'BedGraph adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedGraphAdapter'))).then(r => r.default),
-    }));
-}

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -1,17 +0,0 @@
-import { TabixIndexedFile } from '@gmod/tabix';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature, Region } from '@jbrowse/core/util';
-export default class BedGraphAdapter extends BaseFeatureDataAdapter {
-    private configured?;
-    private configurePre;
-    protected configure(): Promise<{
-        bedGraph: TabixIndexedFile;
-        header: string;
-        columnNames: string[];
-    }>;
-    getNames(): Promise<string[] | undefined>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(): Promise<string>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}