@jbrowse/cli 2.6.2 → 2.7.0

package/lib/types/gff3Adapter.js

@@ -1,23 +1,4 @@
 "use strict";
-var __await = (this && this.__await) || function (v) { return this instanceof __await ? (this.v = v, this) : new __await(v); }
-var __asyncValues = (this && this.__asyncValues) || function (o) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var m = o[Symbol.asyncIterator], i;
-    return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
-    function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
-    function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
-};
-var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var g = generator.apply(thisArg, _arguments || []), i, q = [];
-    return i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i;
-    function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; }
-    function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
-    function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }
-    function fulfill(value) { resume("next", value); }
-    function reject(value) { resume("throw", value); }
-    function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -27,78 +8,63 @@ const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
 const util_1 = require("../util");
-function indexGff3({ config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, }) {
-    return __asyncGenerator(this, arguments, function* indexGff3_1() {
-        var _a, e_1, _b, _c;
-        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 } = yield __await((0, util_1.getLocalOrRemoteStream)(inLocation, outLocation));
-        if (!quiet) {
-            progressBar.start(totalBytes, 0);
+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);
+    }
+    stream.on('data', chunk => {
+        receivedBytes += chunk.length;
+        progressBar.update(receivedBytes);
+    });
+    const rl = readline_1.default.createInterface({
+        input: inLocation.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+    });
+    for await (const line of rl) {
+        if (!line.trim()) {
+            continue;
         }
-        stream.on('data', chunk => {
-            receivedBytes += chunk.length;
-            progressBar.update(receivedBytes);
-        });
-        const rl = readline_1.default.createInterface({
-            input: inLocation.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
-        });
-        try {
-            for (var _d = true, rl_1 = __asyncValues(rl), rl_1_1; rl_1_1 = yield __await(rl_1.next()), _a = rl_1_1.done, !_a; _d = true) {
-                _c = rl_1_1.value;
-                _d = false;
-                const line = _c;
-                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}..${end}`;
-                if (!typesToExclude.includes(type)) {
-                    // turns gff3 attrs into a map, and converts the arrays into space
-                    // separated strings
-                    const col9attrs = Object.fromEntries(col9
-                        .split(';')
-                        .map(f => f.trim())
-                        .filter(f => !!f)
-                        .map(f => f.split('='))
-                        .map(([key, val]) => [
-                        key.trim(),
-                        decodeURIComponent(val).trim().split(',').join(' '),
-                    ]));
-                    const attrs = attributesToIndex
-                        .map(attr => col9attrs[attr])
-                        .filter((f) => !!f);
-                    if (attrs.length) {
-                        const record = JSON.stringify([
-                            encodeURIComponent(locStr),
-                            encodeURIComponent(trackId),
-                            ...attrs.map(a => encodeURIComponent(a)),
-                        ]).replaceAll(',', '|');
-                        yield yield __await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
-                    }
-                }
-            }
+        else if (line.startsWith('#')) {
+            continue;
+        }
+        else if (line.startsWith('>')) {
+            break;
         }
-        catch (e_1_1) { e_1 = { error: e_1_1 }; }
-        finally {
-            try {
-                if (!_d && !_a && (_b = rl_1.return)) yield __await(_b.call(rl_1));
+        const [seq_id, , type, start, end, , , , col9] = line.split('\t');
+        const locStr = `${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(),
+                decodeURIComponent(val).trim().split(',').join(' '),
+            ]));
+            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`;
             }
-            finally { if (e_1) throw e_1.error; }
         }
-        progressBar.stop();
-    });
+    }
+    progressBar.stop();
 }
 exports.indexGff3 = indexGff3;

package/lib/types/vcfAdapter.js

@@ -1,23 +1,4 @@
 "use strict";
-var __await = (this && this.__await) || function (v) { return this instanceof __await ? (this.v = v, this) : new __await(v); }
-var __asyncValues = (this && this.__asyncValues) || function (o) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var m = o[Symbol.asyncIterator], i;
-    return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
-    function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
-    function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
-};
-var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var g = generator.apply(thisArg, _arguments || []), i, q = [];
-    return i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i;
-    function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; }
-    function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
-    function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }
-    function fulfill(value) { resume("next", value); }
-    function reject(value) { resume("throw", value); }
-    function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -27,82 +8,66 @@ const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
 const util_1 = require("../util");
-function indexVcf({ config, attributesToIndex, inLocation, outLocation, quiet, }) {
-    return __asyncGenerator(this, arguments, function* indexVcf_1() {
-        var _a, e_1, _b, _c;
-        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 } = yield __await((0, util_1.getLocalOrRemoteStream)(inLocation, outLocation));
-        if (!quiet) {
-            progressBar.start(totalBytes, 0);
+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);
+    }
+    stream.on('data', chunk => {
+        receivedBytes += chunk.length;
+        progressBar.update(receivedBytes);
+    });
+    const gzStream = inLocation.match(/.b?gz$/)
+        ? stream.pipe((0, zlib_1.createGunzip)())
+        : stream;
+    const rl = readline_1.default.createInterface({
+        input: gzStream,
+    });
+    for await (const line of rl) {
+        if (line.startsWith('#')) {
+            continue;
         }
-        stream.on('data', chunk => {
-            receivedBytes += chunk.length;
-            progressBar.update(receivedBytes);
-        });
-        const gzStream = inLocation.match(/.b?gz$/)
-            ? stream.pipe((0, zlib_1.createGunzip)())
-            : stream;
-        const rl = readline_1.default.createInterface({
-            input: gzStream,
-        });
-        try {
-            for (var _d = true, rl_1 = __asyncValues(rl), rl_1_1; rl_1_1 = yield __await(rl_1.next()), _a = rl_1_1.done, !_a; _d = true) {
-                _c = rl_1_1.value;
-                _d = false;
-                const line = _c;
-                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 ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
-                ]));
-                const end = fields.END;
-                const locStr = `${ref}:${pos}..${end || +pos + 1}`;
-                if (id === '.') {
-                    continue;
-                }
-                const infoAttrs = attributesToIndex
-                    .map(attr => fields[attr])
-                    .filter((f) => !!f);
-                const ids = id.split(',');
-                for (let i = 0; i < ids.length; i++) {
-                    const id = ids[i];
-                    const attrs = [id];
-                    const record = JSON.stringify([
-                        encodeURIComponent(locStr),
-                        encodeURIComponent(trackId),
-                        encodeURIComponent(id || ''),
-                        ...infoAttrs.map(a => encodeURIComponent(a || '')),
-                    ]).replaceAll(',', '|');
-                    yield yield __await(`${record} ${[...new Set(attrs)].join(' ')}\n`);
-                }
-            }
+        // eslint-disable-next-line @typescript-eslint/no-unused-vars
+        const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
+        // turns gff3 attrs into a map, and converts the arrays into space
+        // separated strings
+        const fields = Object.fromEntries(info
+            .split(';')
+            .map(f => f.trim())
+            .filter(f => !!f)
+            .map(f => f.split('='))
+            .map(([key, val]) => [
+            key.trim(),
+            val ? decodeURIComponent(val).trim().split(',').join(' ') : undefined,
+        ]));
+        const end = fields.END;
+        const locStr = `${ref}:${pos}..${end || +pos + 1}`;
+        if (id === '.') {
+            continue;
         }
-        catch (e_1_1) { e_1 = { error: e_1_1 }; }
-        finally {
-            try {
-                if (!_d && !_a && (_b = rl_1.return)) yield __await(_b.call(rl_1));
-            }
-            finally { if (e_1) throw e_1.error; }
+        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();
-    });
+    }
+    progressBar.stop();
 }
 exports.indexVcf = indexVcf;