@apollo-annotation/cli 0.1.15 → 0.1.17

package/README.md

@@ -14,7 +14,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.1.15 linux-x64 node-v18.20.3
+@apollo-annotation/cli/0.1.17 linux-x64 node-v18.20.3
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -82,7 +82,7 @@ EXAMPLES
     $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly
 ```
 
-_See code: [src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
+_See code: [src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
 
 ## `apollo assembly add-gff`
 
@@ -116,7 +116,7 @@ EXAMPLES
     $ apollo assembly add-gff -i genome.gff -a myAssembly -o
 ```
 
-_See code: [src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
+_See code: [src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
 
 ## `apollo assembly check`
 
@@ -158,7 +158,7 @@ EXAMPLES
     $ apollo assembly check -a hg19 -c CDSCheck --delete
 ```
 
-_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/assembly/check.ts)_
+_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/assembly/check.ts)_
 
 ## `apollo assembly delete`
 
@@ -185,7 +185,7 @@ EXAMPLES
     $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f
 ```
 
-_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/assembly/delete.ts)_
+_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
 ## `apollo assembly get`
 
@@ -206,7 +206,7 @@ DESCRIPTION
   Print to stdout the list of assemblies in json format
 ```
 
-_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/assembly/get.ts)_
+_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/assembly/get.ts)_
 
 ## `apollo assembly sequence`
 
@@ -240,7 +240,7 @@ EXAMPLES
     $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000
 ```
 
-_See code: [src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+_See code: [src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
 ## `apollo change get`
 
@@ -264,7 +264,7 @@ DESCRIPTION
   need to use the assembly ID.
 ```
 
-_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/change/get.ts)_
+_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/change/get.ts)_
 
 ## `apollo config [KEY] [VALUE]`
 
@@ -319,7 +319,7 @@ EXAMPLES
     $ apollo config address
 ```
 
-_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/config.ts)_
+_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/config.ts)_
 
 ## `apollo feature add-child`
 
@@ -349,7 +349,7 @@ EXAMPLES
     $ apollo feature add-child -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20
 ```
 
-_See code: [src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/add-child.ts)_
+_See code: [src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
 ## `apollo feature check`
 
@@ -382,7 +382,7 @@ EXAMPLES
     $ apollo feature check -a hg19
 ```
 
-_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/check.ts)_
+_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/check.ts)_
 
 ## `apollo feature copy`
 
@@ -413,7 +413,7 @@ EXAMPLES
     $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38
 ```
 
-_See code: [src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/copy.ts)_
+_See code: [src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/copy.ts)_
 
 ## `apollo feature delete`
 
@@ -437,7 +437,7 @@ DESCRIPTION
   error unless you set -f/--force.
 ```
 
-_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/delete.ts)_
+_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/delete.ts)_
 
 ## `apollo feature edit`
 
@@ -479,7 +479,7 @@ EXAMPLES
     echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j -
 ```
 
-_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/edit.ts)_
+_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/edit.ts)_
 
 ## `apollo feature edit-attribute`
 
@@ -519,7 +519,7 @@ EXAMPLES
     $ apollo feature edit-attribute -i 66...3f -a domains -d
 ```
 
-_See code: [src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+_See code: [src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
 ## `apollo feature edit-coords`
 
@@ -553,7 +553,7 @@ EXAMPLES
     $ apollo feature edit-coords -i abc...xyz -e 2000
 ```
 
-_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
 ## `apollo feature edit-type`
 
@@ -576,7 +576,7 @@ DESCRIPTION
   term although but the valifdity of the new term is not checked.
 ```
 
-_See code: [src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+_See code: [src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
 ## `apollo feature get`
 
@@ -609,7 +609,7 @@ EXAMPLES
     $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000
 ```
 
-_See code: [src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/get.ts)_
+_See code: [src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/get.ts)_
 
 ## `apollo feature get-id`
 
@@ -638,7 +638,7 @@ EXAMPLES
     $ apollo feature get-id -i abc...zyz def...foo
 ```
 
-_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/get-id.ts)_
+_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
 ## `apollo feature import`
 
@@ -666,7 +666,7 @@ EXAMPLES
     $ apollo feature import -d -i features.gff3 -a myAssembly
 ```
 
-_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/import.ts)_
+_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/import.ts)_
 
 ## `apollo feature search`
 
@@ -717,7 +717,7 @@ EXAMPLES
     $ apollo feature search -a mm9 mm10 -t bac
 ```
 
-_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/feature/search.ts)_
+_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/feature/search.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -777,7 +777,7 @@ EXAMPLES
     $ apollo login --profile my-profile
 ```
 
-_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/login.ts)_
+_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/login.ts)_
 
 ## `apollo logout`
 
@@ -806,7 +806,7 @@ EXAMPLES
     $ apollo logout --profile my-profile
 ```
 
-_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/logout.ts)_
+_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/logout.ts)_
 
 ## `apollo refseq get`
 
@@ -838,7 +838,7 @@ EXAMPLES
     $ apollo refseq get -a mm9 mm10
 ```
 
-_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/refseq/get.ts)_
+_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/refseq/get.ts)_
 
 ## `apollo status`
 
@@ -860,7 +860,7 @@ DESCRIPTION
   not check the validity of the access token.
 ```
 
-_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/status.ts)_
+_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/status.ts)_
 
 ## `apollo user get`
 
@@ -895,5 +895,5 @@ EXAMPLES
     $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")'
 ```
 
-_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.15/packages/apollo-cli/src/commands/user/get.ts)_
+_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.17/packages/apollo-cli/src/commands/user/get.ts)_
 <!-- commandsstop -->

package/oclif.manifest.json

@@ -699,6 +699,61 @@
         "get.js"
       ]
     },
+    "refseq:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
+      "examples": [
+        {
+          "description": "All sequences in the database:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Only sequences for these assemblies:",
+          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "refseq:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get reference sequences",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "refseq",
+        "get.js"
+      ]
+    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
@@ -1505,61 +1560,6 @@
         "search.js"
       ]
     },
-    "refseq:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
-      "examples": [
-        {
-          "description": "All sequences in the database:",
-          "command": "<%= config.bin %> <%= command.id %>"
-        },
-        {
-          "description": "Only sequences for these assemblies:",
-          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "assembly": {
-          "char": "a",
-          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "refseq:get",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get reference sequences",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "refseq",
-        "get.js"
-      ]
-    },
     "user:get": {
       "aliases": [],
       "args": {},
@@ -1628,5 +1628,5 @@
       ]
     }
   },
-  "version": "0.1.15"
+  "version": "0.1.17"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@apollo-annotation/cli",
   "description": "Command line interface for the Apollo annotation server",
-  "version": "0.1.15",
+  "version": "0.1.17",
   "author": "Apollo Team",
   "repository": {
     "type": "git",