@jbrowse/cli 2.16.1 → 2.18.0

package/README.md

@@ -57,6 +57,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse make-pif FILE`](#jbrowse-make-pif-file)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
+- [`jbrowse sort-bed FILE`](#jbrowse-sort-bed-file)
 - [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
 - [`jbrowse text-index`](#jbrowse-text-index)
 - [`jbrowse upgrade [LOCALPATH]`](#jbrowse-upgrade-localpath)
@@ -205,7 +206,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -256,7 +257,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -337,7 +338,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -367,7 +368,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -399,7 +400,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -456,7 +457,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -477,7 +478,7 @@ DESCRIPTION
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.16/src/commands/help.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.19/src/commands/help.ts)_
 
 ## `jbrowse make-pif FILE`
 
@@ -507,7 +508,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 
@@ -535,7 +536,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -577,7 +578,38 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+
+## `jbrowse sort-bed FILE`
+
+Helper utility to sort GFF files for tabix. Moves all lines starting with # to
+the top of the file, and sort by refname and start position using unix utilities
+sort and grep
+
+```
+USAGE
+  $ jbrowse sort-bed FILE [-h]
+
+ARGUMENTS
+  FILE  GFF file
+
+FLAGS
+  -h, --help  Show CLI help.
+
+DESCRIPTION
+  Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by
+  refname and start position using unix utilities sort and grep
+
+EXAMPLES
+  # sort gff and pipe to bgzip
+
+  $ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
+
+  $ tabix sorted.gff.gz
+```
+
+_See code:
+[src/commands/sort-bed.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/sort-bed.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -608,7 +640,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -675,7 +707,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -738,7 +770,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.1/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.18.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.js

@@ -6,9 +6,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = require("fs");
 const path_1 = __importDefault(require("path"));
+const core_1 = require("@oclif/core");
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
 const fetchWithProxy_1 = __importDefault(require("./fetchWithProxy"));
 class JBrowseCommand extends core_1.Command {

package/lib/commands/add-assembly.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
+const core_1 = require("@oclif/core");
 const base_1 = __importDefault(require("../base"));
 const { rename, copyFile, mkdir, symlink } = fs_1.default.promises;
 function isValidJSON(string) {

package/lib/commands/add-connection.js

@@ -3,13 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
+const core_1 = require("@oclif/core");
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-// locals
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const base_1 = __importDefault(require("../base"));
+const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 class AddConnection extends base_1.default {
     async run() {
         const { args: runArgs, flags: runFlags } = await this.parse(AddConnection);

package/lib/commands/add-track-json.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = require("fs");
+const core_1 = require("@oclif/core");
 const base_1 = __importDefault(require("../base"));
 class AddTrackJson extends base_1.default {
     async run() {

package/lib/commands/add-track.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
+const core_1 = require("@oclif/core");
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
 const base_1 = __importDefault(require("../base"));
 const { copyFile, rename, symlink } = fs_1.default.promises;

package/lib/commands/admin-server.js

@@ -3,15 +3,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
-const path_1 = __importDefault(require("path"));
-const fs_1 = __importDefault(require("fs"));
 const crypto_1 = __importDefault(require("crypto"));
+const fs_1 = __importDefault(require("fs"));
+const os_1 = __importDefault(require("os"));
+const path_1 = __importDefault(require("path"));
+const core_1 = require("@oclif/core");
 const boxen_1 = __importDefault(require("boxen"));
 const chalk_1 = __importDefault(require("chalk"));
-const os_1 = __importDefault(require("os"));
-const express_1 = __importDefault(require("express"));
 const cors_1 = __importDefault(require("cors"));
+const express_1 = __importDefault(require("express"));
 const base_1 = __importDefault(require("../base"));
 function isValidPort(port) {
     return port > 0 && port < 65535;

package/lib/commands/create.js

@@ -3,11 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
-const base_1 = __importDefault(require("../base"));
+const core_1 = require("@oclif/core");
 const decompress_1 = __importDefault(require("decompress"));
+const base_1 = __importDefault(require("../base"));
+const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const fsPromises = fs_1.default.promises;
 class Create extends base_1.default {
     async run() {

package/lib/commands/make-pif.js

@@ -6,13 +6,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.flipCigar = flipCigar;
 exports.swapIndelCigar = swapIndelCigar;
 exports.createPIF = createPIF;
+const child_process_1 = require("child_process");
 const fs_1 = __importDefault(require("fs"));
+const path_1 = __importDefault(require("path"));
 const readline_1 = __importDefault(require("readline"));
 const zlib_1 = require("zlib");
 const core_1 = require("@oclif/core");
 const command_exists_1 = require("command-exists");
-const child_process_1 = require("child_process");
-const path_1 = __importDefault(require("path"));
 const base_1 = __importDefault(require("../base"));
 const cigarRegex = new RegExp(/([MIDNSHPX=])/);
 function getReadline(filename) {

package/lib/commands/remove-track.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = require("fs");
+const core_1 = require("@oclif/core");
 const base_1 = __importDefault(require("../base"));
 class RemoveTrackJson extends base_1.default {
     async run() {

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

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
+const core_1 = require("@oclif/core");
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
 const base_1 = __importDefault(require("../base"));
 const fsPromises = fs_1.default.promises;

package/lib/commands/sort-bed.js

@@ -0,0 +1,45 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const child_process_1 = require("child_process");
+const core_1 = require("@oclif/core");
+const command_exists_1 = require("command-exists");
+const base_1 = __importDefault(require("../base"));
+class SortGff extends base_1.default {
+    async run() {
+        const { args: { file }, } = await this.parse(SortGff);
+        if ((0, command_exists_1.sync)('sh') &&
+            (0, command_exists_1.sync)('sort') &&
+            (0, command_exists_1.sync)('grep')) {
+            // this command comes from the tabix docs http://www.htslib.org/doc/tabix.html
+            (0, child_process_1.spawn)('sh', [
+                '-c',
+                `(grep "^#" "${file}"; grep -v "^#" "${file}" | sort -t"\`printf '\t'\`" -k1,1 -k2,2n)`,
+            ], {
+                env: { ...process.env, LC_ALL: 'C' },
+                stdio: 'inherit',
+            });
+        }
+        else {
+            throw new Error('Unable to sort, requires unix type environment with sort, grep');
+        }
+    }
+}
+SortGff.description = 'Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep';
+SortGff.examples = [
+    '# sort gff and pipe to bgzip',
+    '$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz',
+    '$ tabix sorted.gff.gz',
+];
+SortGff.args = {
+    file: core_1.Args.string({
+        required: true,
+        description: 'GFF file',
+    }),
+};
+SortGff.flags = {
+    help: core_1.Flags.help({ char: 'h' }),
+};
+exports.default = SortGff;

package/lib/commands/sort-gff.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const child_process_1 = require("child_process");
 const core_1 = require("@oclif/core");
 const command_exists_1 = require("command-exists");
-const child_process_1 = require("child_process");
 const base_1 = __importDefault(require("../base"));
 class SortGff extends base_1.default {
     async run() {

package/lib/commands/text-index.js

@@ -6,13 +6,12 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const stream_1 = require("stream");
-const ixixx_1 = require("ixixx");
 const core_1 = require("@oclif/core");
-// locals
-const gff3Adapter_1 = require("../types/gff3Adapter");
-const vcfAdapter_1 = require("../types/vcfAdapter");
+const ixixx_1 = require("ixixx");
 const base_1 = __importDefault(require("../base"));
 const common_1 = require("../types/common");
+const gff3Adapter_1 = require("../types/gff3Adapter");
+const vcfAdapter_1 = require("../types/vcfAdapter");
 function readConf(path) {
     return JSON.parse(fs_1.default.readFileSync(path, 'utf8'));
 }

package/lib/commands/upgrade.js

@@ -3,12 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
+const core_1 = require("@oclif/core");
 const decompress_1 = __importDefault(require("decompress"));
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const base_1 = __importDefault(require("../base"));
+const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 class Upgrade extends base_1.default {
     async run() {
         const { args: runArgs, flags: runFlags } = await this.parse(Upgrade);

package/lib/types/gff3Adapter.js

@@ -4,9 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexGff3 = indexGff3;
-const cli_progress_1 = require("cli-progress");
-const zlib_1 = require("zlib");
 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;

package/lib/types/vcfAdapter.js

@@ -4,9 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexVcf = indexVcf;
-const cli_progress_1 = require("cli-progress");
-const zlib_1 = require("zlib");
 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;

package/lib/util.js

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
 exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
-const common_1 = require("./types/common");
 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);

package/oclif.manifest.json

@@ -859,6 +859,44 @@
         "set-default-session.js"
       ]
     },
+    "sort-bed": {
+      "aliases": [],
+      "args": {
+        "file": {
+          "description": "GFF file",
+          "name": "file",
+          "required": true
+        }
+      },
+      "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep",
+      "examples": [
+        "# sort gff and pipe to bgzip",
+        "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz",
+        "$ tabix sorted.gff.gz"
+      ],
+      "flags": {
+        "help": {
+          "char": "h",
+          "description": "Show CLI help.",
+          "name": "help",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "sort-bed",
+      "pluginAlias": "@jbrowse/cli",
+      "pluginName": "@jbrowse/cli",
+      "pluginType": "core",
+      "strict": true,
+      "isESM": false,
+      "relativePath": [
+        "lib",
+        "commands",
+        "sort-bed.js"
+      ]
+    },
     "sort-gff": {
       "aliases": [],
       "args": {
@@ -1127,5 +1165,5 @@
       ]
     }
   },
-  "version": "2.16.1"
+  "version": "2.18.0"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -73,5 +73,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }