@jbrowse/cli - npm Package Compare versions

Comparing version 2.7.2 to 2.8.0

lib/commands/add-track.js

@@ -215,7 +215,8 @@ "use strict";
         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?$/i.test(location) ||
@@ -227,3 +228,3 @@ /\.(bw|bigwig)$/i.test(location) ||
             /\.gff3?$/i.test(location) ||
-            /\.chain(.gz)?$/i.test(location)) {
+            /\.chain(\.gz)?$/i.test(location)) {
             return {
@@ -298,2 +299,8 @@ file: location,
         }
+        else if (/\.bedpe(.gz)?$/i.test(location)) {
+            return {
+                type: 'BedpeAdapter',
+                bedpeLocation: makeLocation(location),
+            };
+        }
         else if (/\.bed$/i.test(location)) {
@@ -425,2 +432,3 @@ return {
             VcfAdapter: 'VariantTrack',
+            BedpeAdapter: 'VariantTrack',
             BedAdapter: 'FeatureTrack',
@@ -427,0 +435,0 @@ HicAdapter: 'HicTrack',

oclif.manifest.json

@@ -830,2 +830,32 @@ {
     },
+    "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": {
@@ -1061,3 +1091,3 @@ "aliases": [],
   },
-  "version": "2.7.2"
+  "version": "2.8.0"
 }

package.json

 {
   "name": "@jbrowse/cli",
-  "version": "2.7.2",
+  "version": "2.8.0",
   "description": "A command line tool for working with JBrowse 2",
@@ -53,2 +53,3 @@ "keywords": [
     "cli-progress": "^3.9.0",
+    "command-exists": "^1.2.9",
     "cors": "^2.8.5",
@@ -78,3 +79,3 @@ "decompress": "^4.0.0",
   },
-  "gitHead": "9052b295f2d322e729254457ed9fe2231fb22cce"
+  "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
 }

README.md

@@ -59,2 +59,3 @@ ---
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
+- [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
 - [`jbrowse text-index`](#jbrowse-text-index)
@@ -207,3 +208,3 @@ - [`jbrowse upgrade [LOCALPATH]`](#jbrowse-upgrade-localpath)
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -259,3 +260,3 @@ ## `jbrowse add-connection CONNECTIONURLORPATH`
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -341,3 +342,3 @@ ## `jbrowse add-track TRACK`
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -372,3 +373,3 @@ ## `jbrowse add-track-json TRACK`
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -404,3 +405,3 @@ ## `jbrowse admin-server`
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -462,3 +463,3 @@ ## `jbrowse create LOCALPATH`
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -512,3 +513,3 @@ ## `jbrowse help [COMMANDS]`
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -552,4 +553,32 @@ ## `jbrowse set-default-session`
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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`
@@ -620,3 +649,3 @@
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -684,3 +713,3 @@ ## `jbrowse upgrade [LOCALPATH]`
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.2/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)_
 
@@ -687,0 +716,0 @@ <!-- commandsstop -->

New alerts

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License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Shell access

Supply chain risk

This module accesses the system shell. Accessing the system shell increases the risk of executing arbitrary code.

Found 1 instance in 1 package

Environment variable access

Supply chain risk

Package accesses environment variables, which may be a sign of credential stuffing or data theft.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

190901

increased by1.96%

Number of package files

26

increased by4%

Lines of code

3799

increased by2.15%

Number of lines in readme file

714

increased by4.23%

Worsened metrics

Dependency count

15

increased by7.14%

Number of low supply chain risk alerts

14

increased by7.69%

Number of medium supply chain risk alerts

1

increased byInfinity%

Dependency changes

• + Addedcommand-exists@^1.2.9

• + Addedhas-proto@1.0.3(transitive)

• + Addedhas-symbols@1.0.3(transitive)

• - Removedhas-proto@1.1.0(transitive)

• - Removedhas-symbols@1.1.0(transitive)