@jbrowse/plugin-bed 3.7.0 → 4.0.0

package/dist/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -1,107 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const tabix_1 = require("@gmod/tabix");
-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 rxjs_1 = require("@jbrowse/core/util/rxjs");
-class BedGraphAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre() {
-        const pm = this.pluginManager;
-        const bedGraphGzLocation = this.getConf('bedGraphGzLocation');
-        const location = this.getConf(['index', 'location']);
-        const indexType = this.getConf(['index', 'indexType']);
-        const filehandle = (0, io_1.openLocation)(bedGraphGzLocation, pm);
-        const isCSI = indexType === 'CSI';
-        const bedGraph = new tabix_1.TabixIndexedFile({
-            filehandle,
-            csiFilehandle: isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
-            tbiFilehandle: !isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
-            chunkCacheSize: 50 * 2 ** 20,
-        });
-        const columnNames = this.getConf('columnNames');
-        const header = await bedGraph.getHeader();
-        return {
-            columnNames,
-            bedGraph,
-            header,
-        };
-    }
-    async configure() {
-        if (!this.configured) {
-            this.configured = this.configurePre().catch((e) => {
-                this.configured = undefined;
-                throw e;
-            });
-        }
-        return this.configured;
-    }
-    async getNames() {
-        const { bedGraph, columnNames } = await this.configure();
-        if (columnNames.length) {
-            return columnNames;
-        }
-        const header = await bedGraph.getHeader();
-        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(f => f.trim())
-            : undefined;
-    }
-    async getRefNames(opts = {}) {
-        const { bedGraph } = await this.configure();
-        return bedGraph.getReferenceSequenceNames(opts);
-    }
-    async getHeader() {
-        const { bedGraph } = await this.configure();
-        return bedGraph.getHeader();
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            var _a;
-            const { bedGraph } = await this.configure();
-            const meta = await bedGraph.getMetadata();
-            const { columnNumbers } = meta;
-            const colRef = columnNumbers.ref - 1;
-            const colStart = columnNumbers.start - 1;
-            const colEnd = columnNumbers.end - 1;
-            const same = colStart === colEnd;
-            const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(same ? 2 : 3)) || [];
-            await bedGraph.getLines(query.refName, query.start + (same ? -1 : 0), query.end, {
-                lineCallback: (line, fileOffset) => {
-                    const cols = line.split('\t');
-                    const refName = cols[colRef];
-                    const start = +cols[colStart];
-                    const end = +(same ? start + 1 : cols[colEnd]);
-                    const rest = cols.slice(colEnd + 1);
-                    if (Number.isNaN(start) || Number.isNaN(end)) {
-                        throw new Error(`start/end NaN on line "${line}", with colStart:${colStart} and colEnd:${colEnd}. run "tabix -p bed" to ensure bed preset`);
-                    }
-                    for (let j = 0; j < rest.length; j++) {
-                        const uniqueId = `${this.id}-${fileOffset}-${j}`;
-                        const score = Math.abs(+rest[j]);
-                        const source = names[j] || `col${j}`;
-                        if (score) {
-                            observer.next(new util_1.SimpleFeature({
-                                id: uniqueId,
-                                data: {
-                                    refName,
-                                    start,
-                                    end,
-                                    score,
-                                    source,
-                                },
-                            }));
-                        }
-                    }
-                },
-                ...opts,
-            });
-            observer.complete();
-        });
-    }
-}
-exports.default = BedGraphAdapter;

package/dist/BedGraphTabixAdapter/configSchema.d.ts

@@ -1,29 +0,0 @@
-declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    bedGraphGzLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
-            type: string;
-            defaultValue: string;
-        };
-        location: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    columnNames: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BedGraphTabixAdapter;

package/dist/BedGraphTabixAdapter/configSchema.js

@@ -1,53 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-const BedGraphTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedGraphTabixAdapter', {
-    bedGraphGzLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.bedgraph',
-            locationType: 'UriLocation',
-        },
-    },
-    index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
-        indexType: {
-            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
-            type: 'stringEnum',
-            defaultValue: 'TBI',
-        },
-        location: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.vcf.gz.tbi',
-                locationType: 'UriLocation',
-            },
-        },
-    }),
-    columnNames: {
-        type: 'stringArray',
-        description: 'List of column names',
-        defaultValue: [],
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                bedGraphGzLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                index: {
-                    location: {
-                        uri: `${snap.uri}.tbi`,
-                        baseUri: snap.baseUri,
-                    },
-                },
-            }
-            : snap;
-    },
-});
-exports.default = BedGraphTabixAdapter;

package/dist/BedGraphTabixAdapter/index.d.ts

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

package/dist/BedGraphTabixAdapter/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 = BedGraphTabixAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BedGraphTabixAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'BedGraphTabixAdapter',
-        displayName: 'BedGraphTabix adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedGraphTabixAdapter'))).then(r => r.default),
-    }));
-}

package/dist/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -1,43 +0,0 @@
-import { TabixIndexedFile } from '@gmod/tabix';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import type { Feature, Region } from '@jbrowse/core/util';
-export default class BedTabixAdapter extends BaseFeatureDataAdapter {
-    private parser;
-    protected bed: TabixIndexedFile;
-    protected columnNames: string[];
-    protected scoreColumn: string;
-    static capabilities: string[];
-    setupP?: Promise<{
-        meta: Awaited<ReturnType<TabixIndexedFile['getMetadata']>>;
-    }>;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getMetadataPre2(_opts?: BaseOptions): Promise<{
-        meta: Awaited<ReturnType<TabixIndexedFile["getMetadata"]>>;
-    }>;
-    getMetadataPre(): Promise<{
-        meta: {
-            [key: string]: any;
-            refNameToId: Record<string, number>;
-            refIdToName: string[];
-            metaChar: string | undefined;
-            columnNumbers: {
-                ref: number;
-                start: number;
-                end: number;
-            };
-            coordinateType: string;
-            format: string;
-        };
-    }>;
-    getMetadata(opts?: BaseOptions): Promise<{
-        meta: Awaited<ReturnType<TabixIndexedFile["getMetadata"]>>;
-    }>;
-    getNames(): Promise<string[] | undefined>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -1,104 +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 bed_1 = __importDefault(require("@gmod/bed"));
-const tabix_1 = require("@gmod/tabix");
-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 rxjs_1 = require("@jbrowse/core/util/rxjs");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const util_2 = require("../util");
-class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const bedGzLoc = this.getConf('bedGzLocation');
-        const type = this.getConf(['index', 'indexType']);
-        const loc = this.getConf(['index', 'location']);
-        const autoSql = this.getConf('autoSql');
-        const pm = this.pluginManager;
-        this.bed = new tabix_1.TabixIndexedFile({
-            filehandle: (0, io_1.openLocation)(bedGzLoc, pm),
-            csiFilehandle: type === 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
-            tbiFilehandle: type !== 'CSI' ? (0, io_1.openLocation)(loc, pm) : undefined,
-            chunkCacheSize: 50 * 2 ** 20,
-        });
-        this.columnNames = this.getConf('columnNames');
-        this.scoreColumn = this.getConf('scoreColumn');
-        this.parser = new bed_1.default({ autoSql });
-    }
-    async getRefNames(opts = {}) {
-        return this.bed.getReferenceSequenceNames(opts);
-    }
-    async getHeader(opts) {
-        return this.bed.getHeader(opts);
-    }
-    async getMetadataPre2(_opts) {
-        if (!this.setupP) {
-            this.setupP = this.getMetadataPre().catch((e) => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    async getMetadataPre() {
-        const meta = await this.bed.getMetadata();
-        return { meta };
-    }
-    async getMetadata(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.getMetadataPre2(opts));
-    }
-    async getNames() {
-        if (this.columnNames.length) {
-            return this.columnNames;
-        }
-        const header = await this.getHeader();
-        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(f => f.trim())
-            : undefined;
-    }
-    getFeatures(query, opts) {
-        const { stopToken, statusCallback = () => { } } = opts || {};
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { meta } = await this.getMetadata();
-            const { columnNumbers } = meta;
-            const colRef = columnNumbers.ref - 1;
-            const colStart = columnNumbers.start - 1;
-            const colEnd = columnNumbers.end - 1;
-            const names = await this.getNames();
-            let start = performance.now();
-            (0, stopToken_1.checkStopToken)(stopToken);
-            await (0, util_1.updateStatus)('Downloading features', statusCallback, () => this.bed.getLines(query.refName, query.start, query.end, {
-                lineCallback: (line, fileOffset) => {
-                    if (performance.now() - start > 200) {
-                        (0, stopToken_1.checkStopToken)(stopToken);
-                        start = performance.now();
-                    }
-                    observer.next(new util_1.SimpleFeature((0, util_2.featureData)({
-                        line,
-                        colRef,
-                        colStart,
-                        colEnd,
-                        scoreColumn: this.scoreColumn,
-                        parser: this.parser,
-                        uniqueId: `${this.id}-${fileOffset}`,
-                        names,
-                    })));
-                },
-                stopToken,
-            }));
-            observer.complete();
-        }, stopToken);
-    }
-}
-BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = BedTabixAdapter;

package/dist/BedTabixAdapter/configSchema.d.ts

@@ -1,39 +0,0 @@
-declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    bedGzLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
-            type: string;
-            defaultValue: string;
-        };
-        location: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    columnNames: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-    scoreColumn: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    autoSql: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default BedTabixAdapter;

package/dist/BedTabixAdapter/configSchema.js

@@ -1,63 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
-    bedGzLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.bed.gz',
-            locationType: 'UriLocation',
-        },
-    },
-    index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
-        indexType: {
-            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
-            type: 'stringEnum',
-            defaultValue: 'TBI',
-        },
-        location: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.bed.gz.tbi',
-                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: '',
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                bedGzLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                index: {
-                    location: {
-                        uri: `${snap.uri}.tbi`,
-                        baseUri: snap.baseUri,
-                    },
-                },
-            }
-            : snap;
-    },
-});
-exports.default = BedTabixAdapter;

package/dist/BedTabixAdapter/index.d.ts

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

package/dist/BedTabixAdapter/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 = BedTabixAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function BedTabixAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'BedTabixAdapter',
-        displayName: 'BED tabix adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedTabixAdapter'))).then(r => r.default),
-    }));
-}

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,22 +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 BedpeAdapter extends BaseFeatureDataAdapter {
-    protected bedpeFeatures?: Promise<{
-        header: string;
-        feats1: Record<string, string[]>;
-        feats2: Record<string, string[]>;
-        columnNames: string[];
-    }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
-    static capabilities: string[];
-    private loadDataP;
-    private loadData;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getNames(): Promise<string[] | undefined>;
-    private loadFeatureTreeP;
-    private loadFeatureTree;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-}