@jbrowse/cli 2.5.0 → 2.6.2

package/lib/commands/admin-server.d.ts

@@ -1,13 +0,0 @@
-import { flags } from '@oclif/command';
-import JBrowseCommand from '../base';
-export default class AdminServer extends JBrowseCommand {
-    static description: string;
-    static examples: string[];
-    static flags: {
-        port: flags.IOptionFlag<string | undefined>;
-        root: flags.IOptionFlag<string | undefined>;
-        bodySizeLimit: flags.IOptionFlag<string>;
-        help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
-    };
-    run(): Promise<void>;
-}

package/lib/commands/create.d.ts

@@ -1,23 +0,0 @@
-import { flags } from '@oclif/command';
-import JBrowseCommand from '../base';
-export default class Create extends JBrowseCommand {
-    static description: string;
-    static examples: string[];
-    static args: {
-        name: string;
-        required: boolean;
-        description: string;
-    }[];
-    static flags: {
-        help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
-        force: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        listVersions: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        branch: flags.IOptionFlag<string | undefined>;
-        nightly: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        url: flags.IOptionFlag<string | undefined>;
-        tag: flags.IOptionFlag<string | undefined>;
-    };
-    run(): Promise<void>;
-    checkPath(userPath: string): Promise<void>;
-    catch(error: unknown): Promise<void>;
-}

package/lib/commands/remove-track.d.ts

@@ -1,17 +0,0 @@
-import { flags } from '@oclif/command';
-import JBrowseCommand from '../base';
-export default class RemoveTrackJson extends JBrowseCommand {
-    target: string;
-    static description: string;
-    static examples: string[];
-    static args: {
-        name: string;
-        required: boolean;
-        description: string;
-    }[];
-    static flags: {
-        target: flags.IOptionFlag<string | undefined>;
-        out: flags.IOptionFlag<string | undefined>;
-    };
-    run(): Promise<void>;
-}

package/lib/commands/set-default-session.d.ts

@@ -1,22 +0,0 @@
-import { flags } from '@oclif/command';
-import JBrowseCommand from '../base';
-export default class SetDefaultSession extends JBrowseCommand {
-    private target;
-    static description: string;
-    static examples: string[];
-    static args: never[];
-    static flags: {
-        session: flags.IOptionFlag<string | undefined>;
-        name: flags.IOptionFlag<string>;
-        view: flags.IOptionFlag<string | undefined>;
-        viewId: flags.IOptionFlag<string | undefined>;
-        tracks: flags.IOptionFlag<string | undefined>;
-        currentSession: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        target: flags.IOptionFlag<string | undefined>;
-        out: flags.IOptionFlag<string | undefined>;
-        delete: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
-    };
-    run(): Promise<void>;
-    readDefaultSessionFile(defaultSessionFile: string): Promise<any>;
-}

package/lib/commands/text-index.d.ts

@@ -1,52 +0,0 @@
-/// <reference types="node" />
-import { Readable } from 'stream';
-import { flags } from '@oclif/command';
-import JBrowseCommand, { Track } from '../base';
-export default class TextIndex extends JBrowseCommand {
-    static description: string;
-    static examples: string[];
-    static flags: {
-        help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
-        tracks: flags.IOptionFlag<string | undefined>;
-        target: flags.IOptionFlag<string | undefined>;
-        out: flags.IOptionFlag<string | undefined>;
-        attributes: flags.IOptionFlag<string>;
-        assemblies: flags.IOptionFlag<string | undefined>;
-        force: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        quiet: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        perTrack: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        exclude: flags.IOptionFlag<string>;
-        prefixSize: import("@oclif/parser/lib/flags").IOptionFlag<number | undefined>;
-        file: flags.IOptionFlag<string[]>;
-        fileId: flags.IOptionFlag<string[]>;
-        dryrun: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-    };
-    run(): Promise<void>;
-    aggregateIndex(): Promise<void>;
-    perTrackIndex(): Promise<void>;
-    indexFileList(): Promise<void>;
-    indexDriver({ trackConfigs, attributes, outLocation, name, quiet, typesToExclude, assemblyNames, prefixSize, }: {
-        trackConfigs: Track[];
-        attributes: string[];
-        outLocation: string;
-        name: string;
-        quiet: boolean;
-        typesToExclude: string[];
-        assemblyNames: string[];
-        prefixSize?: number;
-    }): Promise<void>;
-    indexFiles({ trackConfigs, attributes, outLocation, quiet, typesToExclude, }: {
-        trackConfigs: Track[];
-        attributes: string[];
-        outLocation: string;
-        quiet: boolean;
-        typesToExclude: string[];
-    }): AsyncGenerator<string, void, unknown>;
-    runIxIxx({ readStream, outLocation, name, prefixSize, }: {
-        readStream: Readable;
-        outLocation: string;
-        name: string;
-        prefixSize?: number;
-    }): Promise<void>;
-    getTrackConfigs(configPath: string, trackIds?: string[], assemblyName?: string): Promise<Track[]>;
-}

package/lib/commands/upgrade.d.ts

@@ -1,22 +0,0 @@
-import { flags } from '@oclif/command';
-import JBrowseCommand from '../base';
-export default class Upgrade extends JBrowseCommand {
-    static description: string;
-    static examples: string[];
-    static args: {
-        name: string;
-        required: boolean;
-        description: string;
-        default: string;
-    }[];
-    static flags: {
-        help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
-        listVersions: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        tag: flags.IOptionFlag<string | undefined>;
-        branch: flags.IOptionFlag<string | undefined>;
-        nightly: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        clean: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
-        url: flags.IOptionFlag<string | undefined>;
-    };
-    run(): Promise<void>;
-}

package/lib/fetchWithProxy.d.ts

@@ -1,2 +0,0 @@
-import { RequestInfo, RequestInit } from 'node-fetch';
-export default function fetchWithProxy(url: RequestInfo, options?: RequestInit): Promise<import("node-fetch").Response>;

package/lib/index.d.ts

@@ -1 +0,0 @@
-export { run } from '@oclif/command';

package/lib/types/common.d.ts

@@ -1,13 +0,0 @@
-import { Track } from '../base';
-export declare function createRemoteStream(urlIn: string): Promise<import("node-fetch").Response>;
-export declare function isURL(FileName: string): boolean;
-export declare function guessAdapterFromFileName(filePath: string): Track;
-export declare function supported(type: string): boolean;
-export declare function generateMeta({ trackConfigs, attributes, outLocation, name, typesToExclude, assemblyNames, }: {
-    trackConfigs: Track[];
-    attributes: string[];
-    outLocation: string;
-    name: string;
-    typesToExclude: string[];
-    assemblyNames: string[];
-}): Promise<void>;

package/lib/types/gff3Adapter.d.ts

@@ -1,9 +0,0 @@
-import { Track } from '../base';
-export declare function indexGff3({ config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, }: {
-    config: Track;
-    attributesToIndex: string[];
-    inLocation: string;
-    outLocation: string;
-    typesToExclude: string[];
-    quiet: boolean;
-}): AsyncGenerator<string, void, unknown>;

package/lib/types/vcfAdapter.d.ts

@@ -1,9 +0,0 @@
-import { Track } from '../base';
-export declare function indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }: {
-    config: Track;
-    attributesToIndex: string[];
-    inLocation: string;
-    outLocation: string;
-    typesToExclude: string[];
-    quiet: boolean;
-}): AsyncGenerator<string, void, unknown>;

package/lib/util.d.ts

@@ -1,7 +0,0 @@
-/// <reference types="node" />
-/// <reference types="node" />
-import fs from 'fs';
-export declare function getLocalOrRemoteStream(uri: string, out: string): Promise<{
-    totalBytes: number;
-    stream: NodeJS.ReadableStream | fs.ReadStream;
-}>;