@jbrowse/img 3.7.0 → 4.0.1

package/dist/renderRegion.js

@@ -1,385 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.readData = readData;
-exports.renderRegion = renderRegion;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const react_linear_genome_view2_1 = require("@jbrowse/react-linear-genome-view2");
-const util_1 = require("./util");
-function read(file) {
-    let res;
-    try {
-        res = JSON.parse(fs_1.default.readFileSync(file, 'utf8'));
-    }
-    catch (e) {
-        throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`, { cause: e });
-    }
-    return res;
-}
-function makeLocation(file) {
-    return file.startsWith('http') ? { uri: file } : { localPath: file };
-}
-function addRelativePaths(config, configPath) {
-    if (typeof config === 'object') {
-        for (const key of Object.keys(config)) {
-            if (typeof config[key] === 'object') {
-                addRelativePaths(config[key], configPath);
-            }
-            else if (key === 'localPath') {
-                config.localPath = path_1.default.resolve(configPath, config.localPath);
-            }
-        }
-    }
-}
-function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList = [], }) {
-    var _a, _b;
-    const assemblyData = asm && fs_1.default.existsSync(asm) ? read(asm) : undefined;
-    const tracksData = tracks ? read(tracks) : undefined;
-    const configData = config ? read(config) : {};
-    let sessionData = session
-        ? read(session)
-        : undefined;
-    if (config) {
-        addRelativePaths(configData, path_1.default.dirname(path_1.default.resolve(config)));
-    }
-    if (sessionData === null || sessionData === void 0 ? void 0 : sessionData.session) {
-        sessionData = sessionData.session;
-    }
-    if (sessionData === null || sessionData === void 0 ? void 0 : sessionData.views) {
-        sessionData.view = sessionData.views[0];
-    }
-    if (assemblyData) {
-        configData.assembly = assemblyData;
-    }
-    else if ((_a = configData.assemblies) === null || _a === void 0 ? void 0 : _a.length) {
-        configData.assemblies.find(entry => entry.name === asm);
-        if (asm) {
-            const assembly = configData.assemblies.find(entry => entry.name === asm);
-            if (!assembly) {
-                throw new Error(`assembly ${asm} not found in config`);
-            }
-            configData.assembly = assembly;
-        }
-        else {
-            configData.assembly = configData.assemblies[0];
-        }
-    }
-    else if (fasta) {
-        const bgzip = fasta.endsWith('gz');
-        configData.assembly = {
-            name: path_1.default.basename(fasta),
-            sequence: {
-                type: 'ReferenceSequenceTrack',
-                trackId: 'refseq',
-                adapter: {
-                    type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
-                    fastaLocation: makeLocation(fasta),
-                    faiLocation: makeLocation(`${fasta}.fai`),
-                    gziLocation: bgzip ? makeLocation(`${fasta}.gzi`) : undefined,
-                },
-            },
-        };
-        if (aliases) {
-            configData.assembly.refNameAliases = {
-                adapter: {
-                    type: 'RefNameAliasAdapter',
-                    location: makeLocation(aliases),
-                },
-            };
-        }
-        if (cytobands) {
-            configData.assembly.cytobands = {
-                adapter: {
-                    type: 'CytobandAdapter',
-                    location: makeLocation(cytobands),
-                },
-            };
-        }
-    }
-    if (!configData.assembly) {
-        throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
-    }
-    if (tracksData) {
-        configData.tracks = tracksData;
-    }
-    else if (!configData.tracks) {
-        configData.tracks = [];
-    }
-    for (const track of trackList) {
-        const [type, opts] = track;
-        const [file, ...rest] = opts;
-        const index = (_b = rest.find(r => r.startsWith('index:'))) === null || _b === void 0 ? void 0 : _b.replace('index:', '');
-        if (!file) {
-            throw new Error('no file specified');
-        }
-        if (type === 'bam') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'AlignmentsTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BamAdapter',
-                        bamLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${file}.bai`),
-                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'BAI',
-                        },
-                        sequenceAdapter: configData.assembly.sequence.adapter,
-                    },
-                    ...(opts.includes('snpcov')
-                        ? {
-                            displays: [
-                                {
-                                    type: 'LinearSNPCoverageDisplay',
-                                    displayId: `${path_1.default.basename(file)}-${Math.random()}`,
-                                },
-                            ],
-                        }
-                        : {}),
-                },
-            ];
-        }
-        if (type === 'cram') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'AlignmentsTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'CramAdapter',
-                        cramLocation: makeLocation(file),
-                        craiLocation: makeLocation(index || `${file}.crai`),
-                        sequenceAdapter: configData.assembly.sequence.adapter,
-                    },
-                    ...(opts.includes('snpcov')
-                        ? {
-                            displays: [
-                                {
-                                    type: 'LinearSNPCoverageDisplay',
-                                    displayId: `${path_1.default.basename(file)}-${Math.random()}`,
-                                },
-                            ],
-                        }
-                        : {}),
-                },
-            ];
-        }
-        if (type === 'bigwig') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'QuantitativeTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BigWigAdapter',
-                        bigWigLocation: makeLocation(file),
-                    },
-                },
-            ];
-        }
-        if (type === 'vcfgz') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'VariantTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'VcfTabixAdapter',
-                        vcfGzLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${file}.tbi`),
-                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
-                        },
-                    },
-                },
-            ];
-        }
-        if (type === 'gffgz') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'FeatureTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'Gff3TabixAdapter',
-                        gffGzLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${file}.tbi`),
-                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
-                        },
-                    },
-                },
-            ];
-        }
-        if (type === 'hic') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'HicTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'HicAdapter',
-                        hicLocation: makeLocation(file),
-                    },
-                },
-            ];
-        }
-        if (type === 'bigbed') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'FeatureTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BigBedAdapter',
-                        bigBedLocation: makeLocation(file),
-                    },
-                },
-            ];
-        }
-        if (type === 'bedgz') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'FeatureTrack',
-                    trackId: path_1.default.basename(file),
-                    name: path_1.default.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BedTabixAdapter',
-                        bedGzLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${file}.tbi`),
-                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
-                        },
-                    },
-                },
-            ];
-        }
-    }
-    if (!defaultSession) {
-        configData.defaultSession = undefined;
-    }
-    if (sessionData) {
-        configData.defaultSession = sessionData;
-    }
-    return configData;
-}
-function process(trackEntry, view, extra = c => c) {
-    const [, [track, ...opts]] = trackEntry;
-    if (!track) {
-        throw new Error('invalid command line args');
-    }
-    const currentTrack = view.showTrack(extra(track));
-    const display = currentTrack.displays[0];
-    for (const opt of opts) {
-        if (opt.startsWith('height:')) {
-            const [, height] = opt.split(':');
-            if (height) {
-                display.setHeight(+height);
-            }
-        }
-        else if (opt.startsWith('sort:')) {
-            const [, type, tag] = opt.split(':');
-            display.PileupDisplay.setSortedBy(type, tag);
-        }
-        else if (opt.startsWith('color:')) {
-            const [, type, tag] = opt.split(':');
-            if (display.PileupDisplay) {
-                display.PileupDisplay.setColorScheme({ type, tag });
-            }
-            else {
-                display.setColor(type);
-            }
-        }
-        else if (opt.startsWith('force:')) {
-            const [, force] = opt.split(':');
-            if (force) {
-                display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE });
-            }
-        }
-        else if (opt.startsWith('autoscale:')) {
-            const [, autoscale] = opt.split(':');
-            display.setAutoscale(autoscale);
-        }
-        else if (opt.startsWith('minmax:')) {
-            const [, min, max] = opt.split(':');
-            if (min) {
-                display.setMinScore(+min);
-            }
-            if (max) {
-                display.setMaxScore(+max);
-            }
-        }
-        else if (opt.startsWith('scaletype:')) {
-            const [, scaletype] = opt.split(':');
-            display.setScaleType(scaletype);
-        }
-        else if (opt.startsWith('crosshatch:')) {
-            const [, val = 'false'] = opt.split(':');
-            display.setCrossHatches((0, util_1.booleanize)(val));
-        }
-        else if (opt.startsWith('fill:')) {
-            const [, val = 'true'] = opt.split(':');
-            display.setFill((0, util_1.booleanize)(val));
-        }
-        else if (opt.startsWith('resolution:')) {
-            let [, val = 1] = opt.split(':');
-            if (val === 'fine') {
-                val = '10';
-            }
-            else if (val === 'superfine') {
-                val = '100';
-            }
-            display.setResolution(+val);
-        }
-    }
-}
-async function renderRegion(opts) {
-    const model = (0, react_linear_genome_view2_1.createViewState)({
-        ...readData(opts),
-    });
-    const { loc, width = 1500, trackList = [], session: sessionParam, defaultSession, } = opts;
-    const { session } = model;
-    const { view } = session;
-    const { assemblyManager } = model;
-    view.setWidth(width);
-    if (loc) {
-        const { name } = assemblyManager.assemblies[0];
-        if (loc === 'all') {
-            view.showAllRegionsInAssembly(name);
-        }
-        else {
-            await view.navToLocString(loc, name);
-        }
-    }
-    else if (!sessionParam && !defaultSession) {
-        console.warn('No loc specified');
-    }
-    for (const track of trackList) {
-        process(track, view, extra => path_1.default.basename(extra));
-    }
-    return (0, plugin_linear_genome_view_1.renderToSvg)(view, {
-        rasterizeLayers: !opts.noRasterize,
-        ...opts,
-    });
-}

package/dist/setupEnv.d.ts

@@ -1 +0,0 @@
-export default function setupEnv(): void;

package/dist/setupEnv.js

@@ -1,66 +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;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = setupEnv;
-const util_1 = require("util");
-const canvas_1 = require("canvas");
-const jsdom_1 = require("jsdom");
-const node_fetch_1 = __importStar(require("node-fetch"));
-function setupEnv() {
-    addGlobalCanvasUtils();
-    addGlobalTextUtils();
-    addGlobalDocument();
-    addFetchPolyfill();
-}
-function addGlobalCanvasUtils() {
-    global.nodeImage = canvas_1.Image;
-    global.nodeCreateCanvas = canvas_1.createCanvas;
-}
-function addGlobalTextUtils() {
-    global.TextEncoder = util_1.TextEncoder;
-    global.TextDecoder = util_1.TextDecoder;
-}
-function addGlobalDocument() {
-    const window = new jsdom_1.JSDOM('...').window;
-    global.document = window.document;
-    global.window = window;
-    addFetchPolyfill();
-}
-function addFetchPolyfill() {
-    global.fetch = node_fetch_1.default;
-    global.Headers = node_fetch_1.Headers;
-    global.Response = node_fetch_1.Response;
-    global.Request = node_fetch_1.Request;
-}

package/dist/util.d.ts

@@ -1,5 +0,0 @@
-export declare function booleanize(str: string): boolean;
-export declare function convert(result: string, args: {
-    out: string;
-    pngwidth?: string;
-}, spawnArgs?: string[]): void;

package/dist/util.js

@@ -1,30 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.booleanize = booleanize;
-exports.convert = convert;
-const child_process_1 = require("child_process");
-const fs_1 = __importDefault(require("fs"));
-const tmp_1 = __importDefault(require("tmp"));
-function booleanize(str) {
-    return str === 'false' ? false : !!str;
-}
-function createTmp() {
-    return tmp_1.default.fileSync({
-        mode: 0o644,
-        prefix: 'prefix-',
-        postfix: '.svg',
-    });
-}
-function convert(result, args, spawnArgs = []) {
-    const { name } = createTmp();
-    const { pngwidth = '2048', out } = args;
-    fs_1.default.writeFileSync(name, result);
-    const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs];
-    const ls = (0, child_process_1.spawnSync)('rsvg-convert', a);
-    console.error(`rsvg-convert stderr: ${ls.stderr.toString()}`);
-    console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
-    fs_1.default.unlinkSync(name);
-}

package/esm/bin.d.ts

@@ -1,2 +0,0 @@
-#!/usr/bin/env node
-export {};

package/esm/bin.js

@@ -1,11 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-const Module = require('module');
-const originalRequire = Module.prototype.require;
-Module.prototype.require = function (path) {
-    if (path.endsWith('.css')) {
-        return {};
-    }
-    return Reflect.apply(originalRequire, this, arguments);
-};
-require('./index.js');

package/esm/index.d.ts

@@ -1 +0,0 @@
-export {};

package/esm/index.js

@@ -1,141 +0,0 @@
-import fs from 'fs';
-import yargs from 'yargs';
-import { parseArgv, standardizeArgv } from './parseArgv';
-import { renderRegion } from './renderRegion';
-import setupEnv from './setupEnv';
-import { convert } from './util';
-setupEnv();
-const err = console.error;
-console.error = (...p) => {
-    if (!/useLayoutEffect/.exec(`${p[0]}`)) {
-        err(p);
-    }
-};
-const warn = console.warn;
-console.warn = (...p) => {
-    if (!/estimation reached timeout/.exec(`${p[0]}`)) {
-        warn(p);
-    }
-};
-yargs
-    .command('jb2export', 'Creates a jbrowse 2 image snapshot')
-    .option('config', {
-    description: 'Path to config file',
-    type: 'string',
-})
-    .option('session', {
-    description: 'Path to session file',
-    type: 'string',
-})
-    .option('assembly', {
-    description: 'Path to an assembly configuration, or a name of an assembly in the configFile',
-    type: 'string',
-})
-    .option('tracks', {
-    description: 'Path to tracks portion of a session',
-    type: 'string',
-})
-    .option('loc', {
-    description: 'A locstring to navigate to, or --loc all to view the whole genome',
-    type: 'string',
-})
-    .option('fasta', {
-    description: 'Supply a fasta for the assembly',
-    type: 'string',
-})
-    .option('aliases', {
-    description: 'Supply aliases for the assembly, e.g. mapping of 1 to chr1. Tab separated file where column 1 matches the names from the FASTA',
-    type: 'string',
-})
-    .option('width', {
-    description: 'Set the width of the window that jbrowse renders to, default: 1500px',
-    type: 'number',
-})
-    .option('pngwidth', {
-    description: 'Set the width of the png canvas if using png output, default 2048px',
-    type: 'number',
-    default: 2048,
-})
-    .option('configtracks', {
-    description: 'A list of track labels from a config file',
-    type: 'array',
-})
-    .option('bam', {
-    description: 'A bam file, flag --bam can be used multiple times to specify multiple bam files',
-    type: 'array',
-})
-    .option('bigwig', {
-    description: 'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
-    type: 'array',
-})
-    .option('cram', {
-    description: 'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
-    type: 'array',
-})
-    .option('vcfgz', {
-    description: 'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
-    type: 'array',
-})
-    .option('gffgz', {
-    description: 'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
-    type: 'array',
-})
-    .option('hic', {
-    description: 'A .hic file, the --hic can be used multiple times to specify multiple hic files',
-    type: 'array',
-})
-    .option('bigbed', {
-    description: 'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
-    type: 'array',
-})
-    .option('bedgz', {
-    description: 'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
-    type: 'array',
-})
-    .option('out', {
-    description: 'File to output to. Default: out.svg. If a filename with extension .png is supplied the program will try to automatically execute rsvg-convert to convert it to png',
-    type: 'string',
-    default: 'out.svg',
-})
-    .option('noRasterize', {
-    description: 'Use full SVG rendering with no rasterized layers, this can substantially increase filesize',
-    type: 'boolean',
-})
-    .option('defaultSession', {
-    description: 'Use the defaultSession from config.json',
-    type: 'boolean',
-})
-    .help()
-    .alias('help', 'h')
-    .alias('width', 'w').argv;
-const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
-    'bam',
-    'cram',
-    'vcfgz',
-    'hic',
-    'bigwig',
-    'bigbed',
-    'bedgz',
-    'gffgz',
-    'configtracks',
-]);
-(async () => {
-    try {
-        const result = await renderRegion(args);
-        const { out = 'out.svg', pngwidth = '2048' } = args;
-        if (out.endsWith('.png')) {
-            convert(result, { out, pngwidth });
-        }
-        else if (out.endsWith('.pdf')) {
-            convert(result, { out, pngwidth }, ['-f', 'pdf']);
-        }
-        else {
-            fs.writeFileSync(out, result);
-        }
-        process.exit(0);
-    }
-    catch (e) {
-        console.error(e);
-        process.exit(1);
-    }
-})();

package/esm/parseArgv.d.ts

@@ -1,8 +0,0 @@
-export type Entry = [string, string[]];
-export declare function parseArgv(argv: string[]): Entry[];
-export declare function standardizeArgv(args: Entry[], trackTypes: string[]): {
-    [key: string]: unknown;
-    trackList: Entry[];
-    out?: string;
-    pngwidth?: string;
-};

package/esm/parseArgv.js

@@ -1,29 +0,0 @@
-export function parseArgv(argv) {
-    const map = [];
-    while (argv.length) {
-        const val = argv[0].slice(2);
-        argv = argv.slice(1);
-        const next = argv.findIndex(arg => arg.startsWith('-'));
-        if (next !== -1) {
-            map.push([val, argv.slice(0, next)]);
-            argv = argv.slice(next);
-        }
-        else {
-            map.push([val, argv]);
-            break;
-        }
-    }
-    return map;
-}
-export function standardizeArgv(args, trackTypes) {
-    const result = { trackList: [] };
-    for (const arg of args) {
-        if (trackTypes.includes(arg[0])) {
-            result.trackList.push(arg);
-        }
-        else {
-            result[arg[0]] = arg[1][0] || true;
-        }
-    }
-    return result;
-}