@jbrowse/cli 3.5.1 → 3.6.0

package/lib/types/gff3Adapter.js

@@ -1,73 +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.indexGff3 = indexGff3;
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-const cli_progress_1 = require("cli-progress");
-const util_1 = require("../util");
-async function* indexGff3({ config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, }) {
-    const { trackId } = config;
-    // progress bar code was aided by blog post at
-    // https://webomnizz.com/download-a-file-with-progressbar-using-node-js/
-    const progressBar = new cli_progress_1.SingleBar({
-        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
-        etaBuffer: 2000,
-    }, cli_progress_1.Presets.shades_classic);
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, util_1.getLocalOrRemoteStream)(inLocation, outLocation);
-    if (!quiet) {
-        progressBar.start(totalBytes, 0);
-    }
-    // @ts-expect-error
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        progressBar.update(receivedBytes);
-    });
-    const rl = readline_1.default.createInterface({
-        // @ts-expect-error
-        input: /.b?gz$/.exec(inLocation) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
-    });
-    for await (const line of rl) {
-        if (!line.trim()) {
-            continue;
-        }
-        else if (line.startsWith('#')) {
-            continue;
-        }
-        else if (line.startsWith('>')) {
-            break;
-        }
-        const [seq_id, , type, start, end, , , , col9] = line.split('\t');
-        const locStr = `${seq_id}:${start}..${end}`;
-        if (!typesToExclude.includes(type)) {
-            // turns gff3 attrs into a map, and converts the arrays into space
-            // separated strings
-            const col9attrs = Object.fromEntries(col9
-                .split(';')
-                .map(f => f.trim())
-                .filter(f => !!f)
-                .map(f => f.split('='))
-                .map(([key, val]) => [
-                key.trim(),
-                val
-                    ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
-                    : undefined,
-            ]));
-            const attrs = attributesToIndex
-                .map(attr => col9attrs[attr])
-                .filter((f) => !!f);
-            if (attrs.length) {
-                const record = JSON.stringify([
-                    encodeURIComponent(locStr),
-                    encodeURIComponent(trackId),
-                    ...attrs.map(a => encodeURIComponent(a)),
-                ]).replaceAll(',', '|');
-                yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
-            }
-        }
-    }
-    progressBar.stop();
-}

package/lib/types/vcfAdapter.js

@@ -1,76 +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.indexVcf = indexVcf;
-const readline_1 = __importDefault(require("readline"));
-const zlib_1 = require("zlib");
-const cli_progress_1 = require("cli-progress");
-const util_1 = require("../util");
-async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }) {
-    const { trackId } = config;
-    // progress bar code was aided by blog post at
-    // https://webomnizz.com/download-a-file-with-progressbar-using-node-js/
-    const progressBar = new cli_progress_1.SingleBar({
-        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
-        etaBuffer: 2000,
-    }, cli_progress_1.Presets.shades_classic);
-    let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, util_1.getLocalOrRemoteStream)(inLocation, outLocation);
-    if (!quiet) {
-        progressBar.start(totalBytes, 0);
-    }
-    // @ts-expect-error
-    stream.on('data', chunk => {
-        receivedBytes += chunk.length;
-        progressBar.update(receivedBytes);
-    });
-    const gzStream = /.b?gz$/.exec(inLocation)
-        ? // @ts-expect-error
-            stream.pipe((0, zlib_1.createGunzip)())
-        : stream;
-    const rl = readline_1.default.createInterface({
-        input: gzStream,
-    });
-    for await (const line of rl) {
-        if (line.startsWith('#')) {
-            continue;
-        }
-        // eslint-disable-next-line @typescript-eslint/no-unused-vars
-        const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
-        // turns gff3 attrs into a map, and converts the arrays into space
-        // separated strings
-        const fields = Object.fromEntries(info
-            .split(';')
-            .map(f => f.trim())
-            .filter(f => !!f)
-            .map(f => f.split('='))
-            .map(([key, val]) => [
-            key.trim(),
-            val
-                ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
-                : undefined,
-        ]));
-        const end = fields.END;
-        const locStr = `${ref}:${pos}..${end || +pos + 1}`;
-        if (id === '.') {
-            continue;
-        }
-        const infoAttrs = attributesToIndex
-            .map(attr => fields[attr])
-            .filter((f) => !!f);
-        const ids = id.split(',');
-        for (const id of ids) {
-            const attrs = [id];
-            const record = JSON.stringify([
-                encodeURIComponent(locStr),
-                encodeURIComponent(trackId),
-                encodeURIComponent(id || ''),
-                ...infoAttrs.map(a => encodeURIComponent(a || '')),
-            ]).replaceAll(',', '|');
-            yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
-        }
-    }
-    progressBar.stop();
-}

package/lib/util.js

@@ -1,35 +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.getLocalOrRemoteStream = getLocalOrRemoteStream;
-exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const common_1 = require("./types/common");
-async function getLocalOrRemoteStream(uri, out) {
-    if ((0, common_1.isURL)(uri)) {
-        const result = await (0, common_1.createRemoteStream)(uri);
-        return {
-            totalBytes: +(result.headers.get('Content-Length') || 0),
-            stream: result.body,
-        };
-    }
-    else {
-        const filename = path_1.default.isAbsolute(uri) ? uri : path_1.default.join(out, uri);
-        return {
-            totalBytes: fs_1.default.statSync(filename).size,
-            stream: fs_1.default.createReadStream(filename),
-        };
-    }
-}
-function decodeURIComponentNoThrow(uri) {
-    try {
-        return decodeURIComponent(uri);
-    }
-    catch (e) {
-        // avoid throwing exception on a failure to decode URI component
-        return uri;
-    }
-}