@jbrowse/img 3.6.5 → 4.0.0

package/esm/renderRegion.d.ts

@@ -1,34 +0,0 @@
-import type { Entry } from './parseArgv';
-export interface Opts {
-    noRasterize?: boolean;
-    loc?: string;
-    width?: number;
-    session?: string;
-    assembly?: string;
-    config?: string;
-    fasta?: string;
-    aliases?: string;
-    cytobands?: string;
-    defaultSession?: string;
-    trackList?: Entry[];
-    tracks?: string;
-}
-interface Assembly {
-    name: string;
-    sequence: Record<string, unknown>;
-    refNameAliases?: Record<string, unknown>;
-    cytobands?: Record<string, unknown>;
-}
-interface Track {
-    trackId: string;
-    [key: string]: unknown;
-}
-interface Config {
-    assemblies: Assembly[];
-    assembly: Assembly;
-    tracks: Track[];
-    [key: string]: unknown;
-}
-export declare function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList, }: Opts): Config;
-export declare function renderRegion(opts: Opts): Promise<string>;
-export {};

package/esm/renderRegion.js

@@ -1,378 +0,0 @@
-import fs from 'fs';
-import path from 'path';
-import { renderToSvg } from '@jbrowse/plugin-linear-genome-view';
-import { createViewState } from '@jbrowse/react-linear-genome-view2';
-import { booleanize } from './util';
-function read(file) {
-    let res;
-    try {
-        res = JSON.parse(fs.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.resolve(configPath, config.localPath);
-            }
-        }
-    }
-}
-export function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList = [], }) {
-    var _a, _b;
-    const assemblyData = asm && fs.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.dirname(path.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 ${asm} not found in config`);
-            }
-            configData.assembly = assembly;
-        }
-        else {
-            configData.assembly = configData.assemblies[0];
-        }
-    }
-    else if (fasta) {
-        const bgzip = fasta.endsWith('gz');
-        configData.assembly = {
-            name: path.basename(fasta),
-            sequence: {
-                type: 'ReferenceSequenceTrack',
-                trackId: 'refseq',
-                adapter: {
-                    type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
-                    fastaLocation: makeLocation(fasta),
-                    faiLocation: makeLocation(`${fasta}.fai`),
-                    gziLocation: bgzip ? makeLocation(`${fasta}.gzi`) : undefined,
-                },
-            },
-        };
-        if (aliases) {
-            configData.assembly.refNameAliases = {
-                adapter: {
-                    type: 'RefNameAliasAdapter',
-                    location: makeLocation(aliases),
-                },
-            };
-        }
-        if (cytobands) {
-            configData.assembly.cytobands = {
-                adapter: {
-                    type: 'CytobandAdapter',
-                    location: makeLocation(cytobands),
-                },
-            };
-        }
-    }
-    if (!configData.assembly) {
-        throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
-    }
-    if (tracksData) {
-        configData.tracks = tracksData;
-    }
-    else if (!configData.tracks) {
-        configData.tracks = [];
-    }
-    for (const track of trackList) {
-        const [type, opts] = track;
-        const [file, ...rest] = opts;
-        const index = (_b = rest.find(r => r.startsWith('index:'))) === null || _b === void 0 ? void 0 : _b.replace('index:', '');
-        if (!file) {
-            throw new Error('no file specified');
-        }
-        if (type === 'bam') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'AlignmentsTrack',
-                    trackId: path.basename(file),
-                    name: path.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BamAdapter',
-                        bamLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${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: `${path.basename(file)}-${Math.random()}`,
-                                },
-                            ],
-                        }
-                        : {}),
-                },
-            ];
-        }
-        if (type === 'cram') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'AlignmentsTrack',
-                    trackId: path.basename(file),
-                    name: path.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.basename(file)}-${Math.random()}`,
-                                },
-                            ],
-                        }
-                        : {}),
-                },
-            ];
-        }
-        if (type === 'bigwig') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'QuantitativeTrack',
-                    trackId: path.basename(file),
-                    name: path.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BigWigAdapter',
-                        bigWigLocation: makeLocation(file),
-                    },
-                },
-            ];
-        }
-        if (type === 'vcfgz') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'VariantTrack',
-                    trackId: path.basename(file),
-                    name: path.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'VcfTabixAdapter',
-                        vcfGzLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${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.basename(file),
-                    name: path.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'Gff3TabixAdapter',
-                        gffGzLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${file}.tbi`),
-                            indexType: (index === null || index === void 0 ? void 0 : index.endsWith('.csi')) ? 'CSI' : 'TBI',
-                        },
-                    },
-                },
-            ];
-        }
-        if (type === 'hic') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'HicTrack',
-                    trackId: path.basename(file),
-                    name: path.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'HicAdapter',
-                        hicLocation: makeLocation(file),
-                    },
-                },
-            ];
-        }
-        if (type === 'bigbed') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'FeatureTrack',
-                    trackId: path.basename(file),
-                    name: path.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BigBedAdapter',
-                        bigBedLocation: makeLocation(file),
-                    },
-                },
-            ];
-        }
-        if (type === 'bedgz') {
-            configData.tracks = [
-                ...configData.tracks,
-                {
-                    type: 'FeatureTrack',
-                    trackId: path.basename(file),
-                    name: path.basename(file),
-                    assemblyNames: [configData.assembly.name],
-                    adapter: {
-                        type: 'BedTabixAdapter',
-                        bedGzLocation: makeLocation(file),
-                        index: {
-                            location: makeLocation(index || `${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(booleanize(val));
-        }
-        else if (opt.startsWith('fill:')) {
-            const [, val = 'true'] = opt.split(':');
-            display.setFill(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);
-        }
-    }
-}
-export async function renderRegion(opts) {
-    const model = 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.basename(extra));
-    }
-    return renderToSvg(view, {
-        rasterizeLayers: !opts.noRasterize,
-        ...opts,
-    });
-}

package/esm/setupEnv.d.ts

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

package/esm/setupEnv.js

@@ -1,30 +0,0 @@
-import { TextDecoder, TextEncoder } from 'util';
-import { Image, createCanvas } from 'canvas';
-import { JSDOM } from 'jsdom';
-import fetch, { Headers, Request, Response } from 'node-fetch';
-export default function setupEnv() {
-    addGlobalCanvasUtils();
-    addGlobalTextUtils();
-    addGlobalDocument();
-    addFetchPolyfill();
-}
-function addGlobalCanvasUtils() {
-    global.nodeImage = Image;
-    global.nodeCreateCanvas = createCanvas;
-}
-function addGlobalTextUtils() {
-    global.TextEncoder = TextEncoder;
-    global.TextDecoder = TextDecoder;
-}
-function addGlobalDocument() {
-    const window = new JSDOM('...').window;
-    global.document = window.document;
-    global.window = window;
-    addFetchPolyfill();
-}
-function addFetchPolyfill() {
-    global.fetch = fetch;
-    global.Headers = Headers;
-    global.Response = Response;
-    global.Request = Request;
-}

package/esm/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/esm/util.js

@@ -1,23 +0,0 @@
-import { spawnSync } from 'child_process';
-import fs from 'fs';
-import tmp from 'tmp';
-export function booleanize(str) {
-    return str === 'false' ? false : !!str;
-}
-function createTmp() {
-    return tmp.fileSync({
-        mode: 0o644,
-        prefix: 'prefix-',
-        postfix: '.svg',
-    });
-}
-export function convert(result, args, spawnArgs = []) {
-    const { name } = createTmp();
-    const { pngwidth = '2048', out } = args;
-    fs.writeFileSync(name, result);
-    const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs];
-    const ls = spawnSync('rsvg-convert', a);
-    console.error(`rsvg-convert stderr: ${ls.stderr.toString()}`);
-    console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
-    fs.unlinkSync(name);
-}