@jbrowse/cli 4.3.0 → 5.0.0-beta.10

package/dist/commands/make-pif/cigar-utils.js

@@ -1,24 +0,0 @@
-const cigarRegex = new RegExp(/([MIDNSHPX=])/);
-export function parseCigar(cigar = '') {
-    return cigar.split(cigarRegex).slice(0, -1);
-}
-export function flipCigar(cigar) {
-    const arr = [];
-    for (let i = cigar.length - 2; i >= 0; i -= 2) {
-        arr.push(cigar[i]);
-        const op = cigar[i + 1];
-        if (op === 'D') {
-            arr.push('I');
-        }
-        else if (op === 'I') {
-            arr.push('D');
-        }
-        else {
-            arr.push(op);
-        }
-    }
-    return arr;
-}
-export function swapIndelCigar(cigar) {
-    return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
-}

package/dist/commands/make-pif/file-utils.js

@@ -1,30 +0,0 @@
-import fs from 'fs';
-import readline from 'readline';
-import { createGunzip } from 'zlib';
-export function getReadline(filename) {
-    const stream = fs.createReadStream(filename);
-    return readline.createInterface({
-        input: /.b?gz$/.exec(filename) ? stream.pipe(createGunzip()) : stream,
-    });
-}
-export function getStdReadline() {
-    return readline.createInterface({
-        input: process.stdin,
-    });
-}
-export function createWriteWithBackpressure(stream) {
-    return (data) => {
-        // If the stream buffer is full (write returns false), we need to wait for drain
-        if (!stream.write(data)) {
-            return new Promise(resolve => {
-                const drainHandler = () => {
-                    stream.removeListener?.('drain', drainHandler);
-                    resolve();
-                };
-                stream.once?.('drain', drainHandler);
-            });
-        }
-        // If write returns true, the buffer is not full, so we can continue immediately
-        return Promise.resolve();
-    };
-}

package/dist/commands/track-utils.js

@@ -1,74 +0,0 @@
-import path from 'path';
-import { readJsonFile } from "../utils.js";
-import { guessFileNames, guessTrackType, } from "./add-track-utils/adapter-utils.js";
-import { loadFile } from "./add-track-utils/file-operations.js";
-import { buildTrackConfig } from "./add-track-utils/track-config.js";
-import { validateTrackId } from "./add-track-utils/validators.js";
-import { findAndUpdateOrAdd, saveConfigAndReport as saveConfigAndReportBase, } from "./shared/config-operations.js";
-export async function loadTrackConfig(targetConfigPath) {
-    return await readJsonFile(targetConfigPath);
-}
-export async function processTrackFiles({ location, index, bed1, bed2, load, configDir, subDir, force, }) {
-    if (load) {
-        await Promise.all(Object.values(guessFileNames({ location, index, bed1, bed2 }))
-            .filter(f => !!f)
-            .map(src => loadFile({
-            src,
-            destDir: configDir,
-            mode: load,
-            subDir,
-            force,
-        })));
-    }
-}
-export function addTrackToConfig({ configContents, trackConfig, trackId, force, overwrite, }) {
-    validateTrackId(configContents, trackId, force, overwrite);
-    const { updatedItems, wasOverwritten } = findAndUpdateOrAdd({
-        items: configContents.tracks || [],
-        newItem: trackConfig,
-        idField: 'trackId',
-        getId: item => item.trackId,
-        allowOverwrite: force || overwrite || false,
-        itemType: 'track',
-    });
-    return {
-        updatedConfig: { ...configContents, tracks: updatedItems },
-        wasOverwritten,
-    };
-}
-export async function saveTrackConfigAndReport({ config, targetConfigPath, name, trackId, wasOverwritten, }) {
-    await saveConfigAndReportBase({
-        config,
-        target: targetConfigPath,
-        itemType: 'track',
-        itemName: name,
-        itemId: trackId,
-        wasOverwritten,
-    });
-}
-export function buildTrackParams({ flags, location, adapter, configContents, }) {
-    const trackType = flags.trackType || guessTrackType(adapter.type);
-    const trackId = flags.trackId || path.basename(location, path.extname(location));
-    const name = flags.name || trackId;
-    const assemblyNames = flags.assemblyNames || configContents.assemblies?.[0]?.name || '';
-    return {
-        trackType,
-        trackId,
-        name,
-        assemblyNames,
-    };
-}
-export function createTrackConfiguration({ location, trackParams, flags, adapter, configContents, }) {
-    return buildTrackConfig({
-        location,
-        trackType: trackParams.trackType,
-        trackId: trackParams.trackId,
-        name: trackParams.name,
-        assemblyNames: trackParams.assemblyNames,
-        category: flags.category,
-        description: flags.description,
-        config: flags.config,
-        adapter,
-        configContents,
-    });
-}

package/dist/util.js

@@ -1,35 +0,0 @@
-import { createReadStream } from 'fs';
-import { stat } from 'fs/promises';
-import path from 'path';
-import { Readable } from 'stream';
-import { createRemoteStream, isURL } from "./types/common.js";
-export async function getLocalOrRemoteStream(uri, out) {
-    if (isURL(uri)) {
-        const result = await createRemoteStream(uri);
-        return {
-            totalBytes: +(result.headers.get('Content-Length') || 0),
-            stream: result.body,
-        };
-    }
-    else {
-        const filename = path.isAbsolute(uri) ? uri : path.join(out, uri);
-        const stats = await stat(filename);
-        const nodeStream = createReadStream(filename);
-        return {
-            totalBytes: stats.size,
-            stream: Readable.toWeb(nodeStream),
-        };
-    }
-}
-export function decodeURIComponentNoThrow(uri) {
-    if (!uri.includes('%')) {
-        return uri;
-    }
-    try {
-        return decodeURIComponent(uri);
-    }
-    catch {
-        // avoid throwing exception on a failure to decode URI component
-        return uri;
-    }
-}