@jbrowse/cli 2.16.0 → 2.17.0

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/v2.16.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -507,7 +508,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.16.0/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/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/v2.16.0/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.17.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/commands/create.js

@@ -88,7 +88,7 @@ Create.flags = {
         char: 'f',
         description: 'Overwrites existing JBrowse 2 installation if present in path',
     }),
-    // will need to account for pagenation once there is a lot of releases
+    // will need to account for pagination once there is a lot of releases
     listVersions: core_1.Flags.boolean({
         char: 'l',
         description: 'Lists out all versions of JBrowse 2',

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 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() {
+        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/upgrade.js

@@ -83,7 +83,7 @@ Upgrade.args = {
 };
 Upgrade.flags = {
     help: core_1.Flags.help({ char: 'h' }),
-    // will need to account for pagenation once there is a lot of releases
+    // will need to account for pagination once there is a lot of releases
     listVersions: core_1.Flags.boolean({
         char: 'l',
         description: 'Lists out all versions of JBrowse 2',

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": "2.16.0"
+  "version": "2.17.0"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.16.0",
+  "version": "2.17.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -73,5 +73,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }