@jbrowse/cli 2.11.2 → 2.12.1

package/README.md

@@ -67,9 +67,9 @@ Add an assembly to a JBrowse 2 configuration
 
 ```
 USAGE
-  $ jbrowse add-assembly SEQUENCE [-t indexedFasta|bgzipFasta|twoBit|chromSizes|custom] [-n <value>] [-a <value>]
-    [--displayName <value>] [--faiLocation <value>] [--gziLocation <value>] [--refNameAliasesType aliases|custom
-    --refNameAliases <value>] [--refNameColors <value>] [--target <value>] [--out <value>] [-h] [-l
+  $ jbrowse add-assembly SEQUENCE [-t indexedFasta|bgzipFasta|twoBit|chromSizes|custom] [-n <value>] [-a
+    <value>...] [--displayName <value>] [--faiLocation <value>] [--gziLocation <value>] [--refNameAliasesType
+    aliases|custom --refNameAliases <value>] [--refNameColors <value>] [--target <value>] [--out <value>] [-h] [-l
     copy|symlink|move|inPlace] [--skipCheck] [--overwrite] [-f]
 
 ARGUMENTS
@@ -205,7 +205,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -256,7 +256,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -337,7 +337,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -367,7 +367,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -399,7 +399,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -456,7 +456,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -477,7 +477,7 @@ DESCRIPTION
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.22/src/commands/help.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.3/src/commands/help.ts)_
 
 ## `jbrowse make-pif FILE`
 
@@ -507,7 +507,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 
@@ -535,7 +535,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -549,7 +549,8 @@ FLAGS
   -c, --currentSession   List out the current default session
   -h, --help             Show CLI help.
   -n, --name=<value>     [default: New Default Session] Give a name for the default session
-  -s, --session=<value>  set path to a file containing session in json format
+  -s, --session=<value>  set path to a file containing session in json format (required, unless using
+                         delete/currentSession flags)
       --delete           Delete any existing default session.
       --out=<value>      synonym for target
       --target=<value>   path to config file in JB2 installation directory to write out to
@@ -558,17 +559,25 @@ DESCRIPTION
   Set a default session with views and tracks
 
 EXAMPLES
+  # set default session for the config.json in your current directory
+
   $ jbrowse set-default-session --session /path/to/default/session.json
 
-  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json
 
-  $ jbrowse set-default-session --view LinearGenomeView, --name newName
+
+  # make session.json the defaultSession on the specified target config.json file
+
+  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json
+
+
+
+  # print current default session
 
   $ jbrowse set-default-session --currentSession # Prints out current default session
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -599,7 +608,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -608,8 +617,8 @@ Make a text-indexing file for any given track(s).
 ```
 USAGE
   $ jbrowse text-index [-h] [--tracks <value>] [--target <value>] [--out <value>] [--attributes <value>] [-a
-    <value>] [--force] [-q] [--perTrack] [--exclude <value>] [--prefixSize <value>] [--file <value>] [--fileId <value>]
-    [--dryrun]
+    <value>] [--force] [-q] [--perTrack] [--exclude <value>] [--prefixSize <value>] [--file <value>...] [--fileId
+    <value>...] [--dryrun]
 
 FLAGS
   -a, --assemblies=<value>  Specify the assembl(ies) to create an index for. If unspecified, creates an index for each
@@ -666,7 +675,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -729,7 +738,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.11.2/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.12.1/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/commands/create.js

@@ -46,7 +46,7 @@ class Create extends base_1.default {
     async checkPath(userPath) {
         const allFiles = await fsPromises.readdir(userPath);
         if (allFiles.length > 0) {
-            this.error(`${userPath} This directory has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files`, { exit: 120 });
+            this.error(`This directory (${userPath}) has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files`, { exit: 120 });
         }
     }
     async catch(error) {

package/lib/commands/make-pif.js

@@ -3,7 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createPIF = exports.swapIndelCigar = exports.flipCigar = void 0;
+exports.flipCigar = flipCigar;
+exports.swapIndelCigar = swapIndelCigar;
+exports.createPIF = createPIF;
 const fs_1 = __importDefault(require("fs"));
 const readline_1 = __importDefault(require("readline"));
 const zlib_1 = require("zlib");
@@ -44,11 +46,9 @@ function flipCigar(cigar) {
     }
     return arr;
 }
-exports.flipCigar = flipCigar;
 function swapIndelCigar(cigar) {
     return cigar.replaceAll('D', 'K').replaceAll('I', 'D').replaceAll('K', 'I');
 }
-exports.swapIndelCigar = swapIndelCigar;
 async function createPIF(filename, stream) {
     const rl1 = filename ? getReadline(filename) : getStdReadline();
     for await (const line of rl1) {
@@ -65,7 +65,6 @@ async function createPIF(filename, stream) {
     }
     rl1.close();
 }
-exports.createPIF = createPIF;
 class MakePIF extends base_1.default {
     async run() {
         const { args: { file }, flags: { out, csi }, } = await this.parse(MakePIF);

package/lib/commands/set-default-session.js

@@ -25,7 +25,7 @@ class SetDefaultSession extends base_1.default {
             this.exit();
         }
         else if (!session) {
-            this.error(`Please either provide a default session file`, { exit: 120 });
+            this.error(`Please provide a --session file`, { exit: 120 });
         }
         else if (session) {
             await this.writeJsonFile(this.target, {
@@ -59,15 +59,19 @@ class SetDefaultSession extends base_1.default {
 }
 SetDefaultSession.description = 'Set a default session with views and tracks';
 SetDefaultSession.examples = [
+    '# set default session for the config.json in your current directory',
     '$ jbrowse set-default-session --session /path/to/default/session.json',
-    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json',
-    '$ jbrowse set-default-session --view LinearGenomeView, --name newName',
+    '',
+    '# make session.json the defaultSession on the specified target config.json file',
+    '$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json',
+    '',
+    '# print current default session',
     '$ jbrowse set-default-session --currentSession # Prints out current default session',
 ];
 SetDefaultSession.flags = {
     session: core_1.Flags.string({
         char: 's',
-        description: 'set path to a file containing session in json format',
+        description: 'set path to a file containing session in json format (required, unless using delete/currentSession flags)',
     }),
     name: core_1.Flags.string({
         char: 'n',

package/lib/fetchWithProxy.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = fetchWithProxy;
 const node_1 = require("node-fetch-native/node");
 const proxy_1 = require("node-fetch-native/proxy");
 const proxy = (0, proxy_1.createProxy)();
@@ -9,4 +10,3 @@ const proxy = (0, proxy_1.createProxy)();
 function fetchWithProxy(url, options = {}) {
     return (0, node_1.fetch)(url, { ...options, ...proxy });
 }
-exports.default = fetchWithProxy;

package/lib/types/common.js

@@ -3,7 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateMeta = exports.supported = exports.guessAdapterFromFileName = exports.isURL = exports.createRemoteStream = void 0;
+exports.createRemoteStream = createRemoteStream;
+exports.isURL = isURL;
+exports.guessAdapterFromFileName = guessAdapterFromFileName;
+exports.supported = supported;
+exports.generateMeta = generateMeta;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
@@ -14,7 +18,6 @@ async function createRemoteStream(urlIn) {
     }
     return response;
 }
-exports.createRemoteStream = createRemoteStream;
 function isURL(FileName) {
     let url;
     try {
@@ -25,7 +28,6 @@ function isURL(FileName) {
     }
     return url.protocol === 'http:' || url.protocol === 'https:';
 }
-exports.isURL = isURL;
 function makeLocation(location, protocol) {
     if (protocol === 'uri') {
         return {
@@ -104,7 +106,6 @@ function guessAdapterFromFileName(filePath) {
         throw new Error(`Unsupported file type ${filePath}`);
     }
 }
-exports.guessAdapterFromFileName = guessAdapterFromFileName;
 function supported(type) {
     return [
         'Gff3TabixAdapter',
@@ -113,7 +114,6 @@ function supported(type) {
         'VcfAdapter',
     ].includes(type);
 }
-exports.supported = supported;
 async function generateMeta({ trackConfigs, attributes, outLocation, name, typesToExclude, assemblyNames, }) {
     const tracks = trackConfigs.map(({ adapter, textSearching, trackId }) => ({
         trackId,
@@ -127,4 +127,3 @@ async function generateMeta({ trackConfigs, attributes, outLocation, name, types
         assemblyNames,
     }, null, 2));
 }
-exports.generateMeta = generateMeta;

package/lib/types/gff3Adapter.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexGff3 = void 0;
+exports.indexGff3 = indexGff3;
 const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
@@ -69,4 +69,3 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
     }
     progressBar.stop();
 }
-exports.indexGff3 = indexGff3;

package/lib/types/vcfAdapter.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexVcf = void 0;
+exports.indexVcf = indexVcf;
 const cli_progress_1 = require("cli-progress");
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
@@ -74,4 +74,3 @@ async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, q
     }
     progressBar.stop();
 }
-exports.indexVcf = indexVcf;

package/lib/util.js

@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.decodeURIComponentNoThrow = exports.getLocalOrRemoteStream = void 0;
+exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
+exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
 const common_1 = require("./types/common");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
@@ -22,7 +23,6 @@ async function getLocalOrRemoteStream(uri, out) {
     }
     return { totalBytes, stream };
 }
-exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
 function decodeURIComponentNoThrow(uri) {
     try {
         return decodeURIComponent(uri);
@@ -32,4 +32,3 @@ function decodeURIComponentNoThrow(uri) {
         return uri;
     }
 }
-exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;

package/oclif.manifest.json

@@ -783,15 +783,19 @@
       "args": {},
       "description": "Set a default session with views and tracks",
       "examples": [
+        "# set default session for the config.json in your current directory",
         "$ jbrowse set-default-session --session /path/to/default/session.json",
-        "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json",
-        "$ jbrowse set-default-session --view LinearGenomeView, --name newName",
+        "",
+        "# make session.json the defaultSession on the specified target config.json file",
+        "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json",
+        "",
+        "# print current default session",
         "$ jbrowse set-default-session --currentSession # Prints out current default session"
       ],
       "flags": {
         "session": {
           "char": "s",
-          "description": "set path to a file containing session in json format",
+          "description": "set path to a file containing session in json format (required, unless using delete/currentSession flags)",
           "name": "session",
           "hasDynamicHelp": false,
           "multiple": false,
@@ -1123,5 +1127,5 @@
       ]
     }
   },
-  "version": "2.11.2"
+  "version": "2.12.1"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.11.2",
+  "version": "2.12.1",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -45,7 +45,7 @@
     "docs:version:add": "git add README.md"
   },
   "dependencies": {
-    "@oclif/core": "^3.22.0",
+    "@oclif/core": "^4.0.6",
     "@oclif/plugin-help": "^6.0.15",
     "boxen": "^4.2.0",
     "chalk": "^4.1.0",
@@ -74,5 +74,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
+  "gitHead": "20f16ae5a56ae5e4806aaa373131e540b0b5b0fd"
 }