@jbrowse/cli 4.0.4 → 4.1.3

package/dist/types/gff3Adapter.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexGff3 = indexGff3;
-const util_ts_1 = require("../util.js");
-const streamUtils_ts_1 = require("./streamUtils.js");
-async function* indexGff3({ config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, }) {
-    const { trackId } = config;
-    const { rl, progressBar } = await (0, streamUtils_ts_1.createIndexingStream)({
-        inLocation,
-        outLocation,
-        trackId,
-        quiet,
-    });
-    const excludeSet = new Set(typesToExclude);
-    const encodedTrackId = encodeURIComponent(trackId);
-    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');
-        if (!excludeSet.has(type)) {
-            const col9attrs = (0, streamUtils_ts_1.parseAttributes)(col9, util_ts_1.decodeURIComponentNoThrow);
-            const attrs = attributesToIndex
-                .map(attr => col9attrs[attr])
-                .filter((f) => !!f);
-            if (attrs.length > 0) {
-                const locStr = `${seq_id}:${start}..${end}`;
-                const encodedAttrs = attrs.map(a => `"${encodeURIComponent(a)}"`);
-                const record = `["${encodeURIComponent(locStr)}"|"${encodedTrackId}"|${encodedAttrs.join('|')}]`;
-                const uniqueAttrs = [...new Set(attrs)];
-                yield `${record} ${uniqueAttrs.join(' ')}\n`;
-            }
-        }
-    }
-    progressBar.stop();
-}

package/dist/types/streamUtils.js

@@ -1,66 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.createIndexingStream = createIndexingStream;
-exports.parseAttributes = parseAttributes;
-const cli_progress_1 = require("cli-progress");
-const util_ts_1 = require("../util.js");
-async function* readLines(reader, progressBar) {
-    const decoder = new TextDecoder();
-    let buffer = '';
-    let receivedBytes = 0;
-    try {
-        let result = await reader.read();
-        while (!result.done) {
-            receivedBytes += result.value.length;
-            progressBar.update(receivedBytes);
-            buffer += decoder.decode(result.value, { stream: true });
-            const lines = buffer.split('\n');
-            buffer = lines.pop();
-            for (const line of lines) {
-                yield line;
-            }
-            result = await reader.read();
-        }
-    }
-    finally {
-        reader.releaseLock();
-    }
-    buffer += decoder.decode();
-    if (buffer) {
-        yield buffer;
-    }
-}
-async function createIndexingStream({ inLocation, outLocation, trackId, quiet, }) {
-    const progressBar = new cli_progress_1.SingleBar({
-        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
-        etaBuffer: 2000,
-    }, cli_progress_1.Presets.shades_classic);
-    const { totalBytes, stream } = await (0, util_ts_1.getLocalOrRemoteStream)(inLocation, outLocation);
-    if (!quiet) {
-        progressBar.start(totalBytes, 0);
-    }
-    if (!stream) {
-        throw new Error(`Failed to fetch ${inLocation}: no response body`);
-    }
-    const inputStream = /.b?gz$/.exec(inLocation)
-        ? // @ts-ignore root tsconfig includes DOM lib which has incompatible stream types
-            stream.pipeThrough(new DecompressionStream('gzip'))
-        : stream;
-    const rl = readLines(inputStream.getReader(), progressBar);
-    return { rl, progressBar };
-}
-function parseAttributes(infoString, decodeFunc) {
-    const result = {};
-    for (const field of infoString.split(';')) {
-        const trimmed = field.trim();
-        if (trimmed) {
-            const eqIdx = trimmed.indexOf('=');
-            if (eqIdx !== -1) {
-                const key = trimmed.slice(0, eqIdx).trim();
-                const val = trimmed.slice(eqIdx + 1);
-                result[key] = decodeFunc(val).trim().replaceAll(',', ' ');
-            }
-        }
-    }
-    return result;
-}

package/dist/types/vcfAdapter.js

@@ -1,39 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexVcf = indexVcf;
-const util_ts_1 = require("../util.js");
-const streamUtils_ts_1 = require("./streamUtils.js");
-async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }) {
-    const { trackId } = config;
-    const { rl, progressBar } = await (0, streamUtils_ts_1.createIndexingStream)({
-        inLocation,
-        outLocation,
-        trackId,
-        quiet,
-    });
-    const encodedTrackId = encodeURIComponent(trackId);
-    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');
-        if (id === '.') {
-            continue;
-        }
-        const fields = (0, streamUtils_ts_1.parseAttributes)(info, util_ts_1.decodeURIComponentNoThrow);
-        const end = fields.END;
-        const locStr = `${ref}:${pos}..${end || +pos + 1}`;
-        const encodedLocStr = encodeURIComponent(locStr);
-        const infoAttrs = attributesToIndex
-            .map(attr => fields[attr])
-            .filter((f) => !!f);
-        const encodedInfoAttrs = infoAttrs.map(a => `"${encodeURIComponent(a)}"`);
-        for (const variantId of id.split(',')) {
-            const encodedId = encodeURIComponent(variantId);
-            const record = `["${encodedLocStr}"|"${encodedTrackId}"|"${encodedId}"${encodedInfoAttrs.length > 0 ? `|${encodedInfoAttrs.join('|')}` : ''}]`;
-            yield `${record} ${variantId}\n`;
-        }
-    }
-    progressBar.stop();
-}