@jbrowse/cli 2.7.1 → 2.8.0

package/README.md

@@ -56,6 +56,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`jbrowse help [COMMANDS]`](#jbrowse-help-commands)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
+- [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
 - [`jbrowse text-index`](#jbrowse-text-index)
 - [`jbrowse upgrade [LOCALPATH]`](#jbrowse-upgrade-localpath)
 
@@ -203,7 +204,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -254,7 +255,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -335,7 +336,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -365,7 +366,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -396,7 +397,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -453,7 +454,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMANDS]`
 
@@ -502,7 +503,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -541,7 +542,35 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
+
+## `jbrowse sort-gff 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-gff FILE
+
+ARGUMENTS
+  FILE  GFF file
+
+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-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -608,7 +637,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -671,7 +700,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.1/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.8.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/commands/add-track.js

@@ -212,18 +212,19 @@ class AddTrack extends base_1.default {
             };
         }
         else if (/\.2bit$/i.test(location) ||
+            /\.bedpe(\.gz)?$/i.test(location) ||
             /\/trackData.jsonz?$/i.test(location) ||
             /\/sparql$/i.test(location) ||
-            /\.out(.gz)?$/i.test(location) ||
-            /\.paf(.gz)?$/i.test(location) ||
-            /\.delta(.gz)?$/i.test(location) ||
+            /\.out(\.gz)?$/i.test(location) ||
+            /\.paf(\.gz)?$/i.test(location) ||
+            /\.delta(\.gz)?$/i.test(location) ||
             /\.bed?$/i.test(location) ||
             /\.(bw|bigwig)$/i.test(location) ||
             /\.(bb|bigbed)$/i.test(location) ||
             /\.vcf$/i.test(location) ||
             /\.gtf?$/i.test(location) ||
             /\.gff3?$/i.test(location) ||
-            /\.chain(.gz)?$/i.test(location)) {
+            /\.chain(\.gz)?$/i.test(location)) {
             return {
                 file: location,
             };
@@ -293,6 +294,12 @@ class AddTrack extends base_1.default {
                 type: 'UNSUPPORTED',
             };
         }
+        else if (/\.bedpe(.gz)?$/i.test(location)) {
+            return {
+                type: 'BedpeAdapter',
+                bedpeLocation: makeLocation(location),
+            };
+        }
         else if (/\.bed$/i.test(location)) {
             return {
                 type: 'BedAdapter',
@@ -419,6 +426,7 @@ class AddTrack extends base_1.default {
             TwoBitAdapter: 'ReferenceSequenceTrack',
             VcfTabixAdapter: 'VariantTrack',
             VcfAdapter: 'VariantTrack',
+            BedpeAdapter: 'VariantTrack',
             BedAdapter: 'FeatureTrack',
             HicAdapter: 'HicTrack',
             PAFAdapter: 'SyntenyTrack',

package/lib/commands/sort-gff.js

@@ -0,0 +1,42 @@
+"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 -k4,4n)`,
+            ], {
+                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`,
+    }),
+};
+exports.default = SortGff;

package/oclif.manifest.json

@@ -827,6 +827,36 @@
         "set-default-session.js"
       ]
     },
+    "sort-gff": {
+      "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": {},
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "sort-gff",
+      "pluginAlias": "@jbrowse/cli",
+      "pluginName": "@jbrowse/cli",
+      "pluginType": "core",
+      "strict": true,
+      "isESM": false,
+      "relativePath": [
+        "lib",
+        "commands",
+        "sort-gff.js"
+      ]
+    },
     "text-index": {
       "aliases": [],
       "args": {},
@@ -1057,5 +1087,5 @@
       ]
     }
   },
-  "version": "2.7.1"
+  "version": "2.8.0"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.7.1",
+  "version": "2.8.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -50,6 +50,7 @@
     "boxen": "^4.2.0",
     "chalk": "^4.1.0",
     "cli-progress": "^3.9.0",
+    "command-exists": "^1.2.9",
     "cors": "^2.8.5",
     "decompress": "^4.0.0",
     "express": "^4.17.1",
@@ -74,5 +75,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "2cda1611eebd12517f2a3cfc1b612face27005d4"
+  "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
 }