@apollo-annotation/cli 0.1.10

package/oclif.manifest.json

@@ -0,0 +1,1632 @@
+{
+  "commands": {
+    "config": {
+      "aliases": [],
+      "args": {
+        "key": {
+          "description": "Name of configuration parameter",
+          "name": "key"
+        },
+        "value": {
+          "description": "Parameter value",
+          "name": "value"
+        }
+      },
+      "description": "Use this command to create or edit a user profile with credentials to access\nApollo. Configuration options are:\n\n - address:\nAddress and port e.g http://localhost:3999\n\n- accessType:\nHow to access Apollo. accessType is typically one of: google, microsoft, guest,\nroot. Allowed types depend on your Apollo setup\n\n- accessToken:\nAccess token. Usually inserted by `apollo login`\n\n- rootCredentials.username:\nUsername of root account. Only set this for \"root\" access type\n\n- rootCredentials.password:\nPassword for root account. Only set this for \"root\" access type",
+      "examples": [
+        {
+          "description": "Interactive setup:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Setup with key/value pairs:",
+          "command": "<%= config.bin %> <%= command.id %> --profile admin address http://localhost:3999"
+        },
+        {
+          "description": "Get current address for default profile:",
+          "command": "<%= config.bin %> <%= command.id %> address"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Profile to create or edit",
+          "name": "profile",
+          "required": false,
+          "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"
+        },
+        "get-config-file": {
+          "description": "Return the path to the config file and exit (this file may not exist yet)",
+          "name": "get-config-file",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "config",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get or set apollo configuration options",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "config.js"
+      ]
+    },
+    "login": {
+      "aliases": [],
+      "args": {},
+      "description": "Use the provided credentials to obtain and save the token to access Apollo. Once\nthe token for the given profile has been saved in the configuration file, users\ndo not normally need to execute this command again unless the token has expired.\nTo setup a new profile use \"apollo config\"",
+      "examples": [
+        {
+          "description": "The most basic and probably most typical usage is to login using the default\nprofile in configuration file:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Login with a different profile:",
+          "command": "<%= config.bin %> <%= command.id %> --profile my-profile"
+        }
+      ],
+      "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"
+        },
+        "address": {
+          "char": "a",
+          "description": "Address of Apollo server",
+          "name": "address",
+          "required": false,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "username": {
+          "char": "u",
+          "description": "Username for root login",
+          "name": "username",
+          "required": false,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "password": {
+          "char": "p",
+          "description": "Password for <username>",
+          "name": "password",
+          "required": false,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "force": {
+          "char": "f",
+          "description": "Force re-authentication even if user is already logged in",
+          "name": "force",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "port": {
+          "description": "Get token by listening to this port number (usually this is >= 1024 and < 65536)",
+          "name": "port",
+          "default": 3000,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "login",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Login to Apollo",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "login.js"
+      ]
+    },
+    "logout": {
+      "aliases": [],
+      "args": {},
+      "description": "Logout by removing the access token from the selected profile",
+      "examples": [
+        {
+          "description": "Logout default profile:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Logout selected profile",
+          "command": "<%= config.bin %> <%= command.id %> --profile my-profile"
+        }
+      ],
+      "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"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "logout",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Logout of Apollo",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "logout.js"
+      ]
+    },
+    "status": {
+      "aliases": [],
+      "args": {},
+      "description": "This command returns \"<profile>: Logged in\" if the selected profile has an\naccess token and \"<profile>: Logged out\" otherwise. Note that this command does\nnot check the validity of the access token.",
+      "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"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "status",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "View authentication status",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "status.js"
+      ]
+    },
+    "assembly:add-fasta": {
+      "aliases": [],
+      "args": {},
+      "description": "Add new assembly from local or external fasta file",
+      "examples": [
+        {
+          "description": "From local file:",
+          "command": "<%= config.bin %> <%= command.id %> -i genome.fa -a myAssembly"
+        },
+        {
+          "description": "From external source we also need the URL of the index:",
+          "command": "<%= config.bin %> <%= command.id %> -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly"
+        }
+      ],
+      "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"
+        },
+        "input-file": {
+          "char": "i",
+          "description": "Input fasta file",
+          "name": "input-file",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Name for this assembly. Use the file name if omitted",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "index": {
+          "char": "x",
+          "description": "URL of the index. Required if input is an external source and ignored if input is a local file",
+          "name": "index",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "force": {
+          "char": "f",
+          "description": "Delete existing assembly, if it exists",
+          "name": "force",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "assembly:add-fasta",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "assembly",
+        "add-fasta.js"
+      ]
+    },
+    "assembly:add-gff": {
+      "aliases": [],
+      "args": {},
+      "description": "The gff file is expected to contain sequences as per gff specifications.\nFeatures are also imported by default.",
+      "examples": [
+        {
+          "description": "Import sequences and features:",
+          "command": "<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly"
+        },
+        {
+          "description": "Import sequences only:",
+          "command": "<%= config.bin %> <%= command.id %> -i genome.gff -a myAssembly -o"
+        }
+      ],
+      "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"
+        },
+        "input-file": {
+          "char": "i",
+          "description": "Input gff or gtf file",
+          "name": "input-file",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Name for this assembly. Use the file name if omitted",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "omit-features": {
+          "char": "o",
+          "description": "Do not import features, only upload the sequences",
+          "name": "omit-features",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "force": {
+          "char": "f",
+          "description": "Delete existing assembly, if it exists",
+          "name": "force",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "assembly:add-gff",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Add new assembly from gff or gft file",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "assembly",
+        "add-gff.js"
+      ]
+    },
+    "assembly:check": {
+      "aliases": [],
+      "args": {},
+      "description": "Manage checks, i.e. the rules ensuring features in an assembly are plausible.\nThis command only sets the check to apply, to retrieve features flagged by these\nchecks use `apollo feature check`.",
+      "examples": [
+        {
+          "description": "View available check types:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "View checks set for assembly hg19:",
+          "command": "<%= config.bin %> <%= command.id %> -a hg19"
+        },
+        {
+          "description": "Add checks to assembly:",
+          "command": "<%= config.bin %> <%= command.id %> -a hg19 -c CDSCheck"
+        },
+        {
+          "description": "Delete checks from assembly:",
+          "command": "<%= config.bin %> <%= command.id %> -a hg19 -c CDSCheck --delete"
+        }
+      ],
+      "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": "Manage checks in this assembly",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "check": {
+          "char": "c",
+          "description": "Add these check names or IDs. If unset, print the checks set for assembly",
+          "name": "check",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        },
+        "delete": {
+          "char": "d",
+          "description": "Delete (instead of adding) checks",
+          "name": "delete",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "assembly:check",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Add, view, or delete checks to assembly",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "assembly",
+        "check.js"
+      ]
+    },
+    "assembly:delete": {
+      "aliases": [],
+      "args": {},
+      "description": "Assemblies to delete may be names or IDs",
+      "examples": [
+        {
+          "description": "Delete multiple assemblies using name or ID:",
+          "command": "<%= config.bin %> <%= command.id %> -a mouse 6605826fbd0eee691f83e73f"
+        }
+      ],
+      "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": "Assembly names or IDs to delete",
+          "name": "assembly",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        },
+        "verbose": {
+          "char": "v",
+          "description": "Print to stdout the array of assemblies deleted",
+          "name": "verbose",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "assembly:delete",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Delete assemblies",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "assembly",
+        "delete.js"
+      ]
+    },
+    "assembly:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Print to stdout the list of assemblies in json format",
+      "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 assemblies in this list of names or IDs",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "assembly:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get available assemblies",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "assembly",
+        "get.js"
+      ]
+    },
+    "assembly:sequence": {
+      "aliases": [],
+      "args": {},
+      "description": "Return the reference sequence for a given assembly and coordinates",
+      "examples": [
+        {
+          "description": "Get all sequences in myAssembly:",
+          "command": "<%= config.bin %> <%= command.id %> -a myAssembly"
+        },
+        {
+          "description": "Get sequence in coordinates chr1:1..1000:",
+          "command": "<%= config.bin %> <%= command.id %> -a myAssembly -r chr1 -s 1 -e 1000"
+        }
+      ],
+      "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": "Find input reference sequence in this assembly",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "refseq": {
+          "char": "r",
+          "description": "Reference sequence. If unset, get all sequences",
+          "name": "refseq",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "Start coordinate (1-based)",
+          "name": "start",
+          "default": 1,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "end": {
+          "char": "e",
+          "description": "End coordinate",
+          "name": "end",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "assembly:sequence",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get reference sequence in fasta format",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "assembly",
+        "sequence.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": {},
+      "description": "If set, filters username and role must be both satisfied to return an entry",
+      "examples": [
+        {
+          "description": "By username:",
+          "command": "<%= config.bin %> <%= command.id %> -u Guest"
+        },
+        {
+          "description": "By role:",
+          "command": "<%= config.bin %> <%= command.id %> -r admin"
+        },
+        {
+          "description": "Use jq for more control:",
+          "command": "<%= config.bin %> <%= command.id %> | jq '.[] | select(.createdAt > \"2024-03-18\")'"
+        }
+      ],
+      "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"
+        },
+        "username": {
+          "char": "u",
+          "description": "Find this username",
+          "name": "username",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "role": {
+          "char": "r",
+          "description": "Get users with this role",
+          "name": "role",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "user:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get list of users",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "user",
+        "get.js"
+      ]
+    },
+    "change:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Return the change log in json format. Note that when an assembly is deleted the\nlink between common name and ID is lost (it can still be recovered by inspecting\nthe change log but at present this task is left to the user). In such cases you\nneed to use the assembly ID.",
+      "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 changes only for these assembly names or IDs (but see description)",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "change:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get list of changes",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "change",
+        "get.js"
+      ]
+    },
+    "feature:add-child": {
+      "aliases": [],
+      "args": {},
+      "description": "See the other commands under `apollo feature` to retrive the parent ID of\ninterest and to populate the child feature with attributes.",
+      "examples": [
+        {
+          "description": "Add an exon at genomic coordinates 10..20 to this feature ID:",
+          "command": "<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20"
+        }
+      ],
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Add a child to this feature ID; use - to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "Start coordinate of the child feature (1-based)",
+          "name": "start",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "end": {
+          "char": "e",
+          "description": "End coordinate of the child feature (1-based)",
+          "name": "end",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "type": {
+          "char": "t",
+          "description": "Type of child feature",
+          "name": "type",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:add-child",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Add a child feature (e.g. add an exon to an mRNA)",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "add-child.js"
+      ]
+    },
+    "feature:check": {
+      "aliases": [],
+      "args": {},
+      "description": "Use this command to view which features fail checks along with the reason for\nfailing. Use `apollo assembly check` for managing which checks should be applied\nto an assembly",
+      "examples": [
+        {
+          "description": "Get all check results in the database:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Get check results for assembly hg19:",
+          "command": "<%= config.bin %> <%= command.id %> -a hg19"
+        }
+      ],
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Get checks for these feature identifiers",
+          "name": "feature-id",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get checks for this assembly",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:check",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get check results",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "check.js"
+      ]
+    },
+    "feature:copy": {
+      "aliases": [],
+      "args": {},
+      "description": "The feature may be copied to the same or to a different assembly. he destination\nreference sequence may be selected by name only if unique in the database or by\nname and assembly or by identifier.",
+      "examples": [
+        {
+          "description": "Copy this feature ID to chr1:100 in assembly hg38:",
+          "command": "<%= config.bin %> <%= command.id %> -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38"
+        }
+      ],
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to copy to; use - to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "refseq": {
+          "char": "r",
+          "description": "Name or ID of target reference sequence",
+          "name": "refseq",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "Start position in target reference sequence",
+          "name": "start",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Name or ID of target assembly. Not required if refseq is unique in the database",
+          "name": "assembly",
+          "required": false,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:copy",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Copy a feature to another location",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "copy.js"
+      ]
+    },
+    "feature:delete": {
+      "aliases": [],
+      "args": {},
+      "description": "Note that deleting a child feature after deleting its parent will result in an\nerror unless you set -f/--force.",
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature IDs to delete",
+          "name": "feature-id",
+          "default": [
+            "-"
+          ],
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        },
+        "force": {
+          "char": "f",
+          "description": "Ignore non-existing features",
+          "name": "force",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "dry-run": {
+          "char": "n",
+          "description": "Only show what would be delete",
+          "name": "dry-run",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:delete",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Delete one or more features by ID",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "delete.js"
+      ]
+    },
+    "feature:edit-attribute": {
+      "aliases": [],
+      "args": {},
+      "description": "Be aware that there is no checking whether attributes names and values are\nvalid. For example, you can create non-unique ID attributes or you can set gene\nontology terms to non-existing terms",
+      "examples": [
+        {
+          "description": "Add attribute \"domains\" with a list of values:",
+          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -v ABC PLD"
+        },
+        {
+          "description": "Print values in \"domains\" as json array:",
+          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains"
+        },
+        {
+          "description": "Delete attribute \"domains\"",
+          "command": "<%= config.bin %> <%= command.id %> -i 66...3f -a domains -d"
+        }
+      ],
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "attribute": {
+          "char": "a",
+          "description": "Attribute key to add or edit",
+          "name": "attribute",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "value": {
+          "char": "v",
+          "description": "New attribute value. Separated mutliple values by space to them as a list. If unset return current value",
+          "name": "value",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        },
+        "delete": {
+          "char": "d",
+          "description": "Delete this attribute",
+          "name": "delete",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:edit-attribute",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Add, edit, or view a feature attribute",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "edit-attribute.js"
+      ]
+    },
+    "feature:edit-coords": {
+      "aliases": [],
+      "args": {},
+      "description": "If editing a child feature that new coordinates must be within the parent's\ncoordinates. To get the identifier of the feature to edit consider using `apollo\nfeature get` or `apollo feature search`",
+      "examples": [
+        {
+          "description": "Edit start and end:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -s 10 -e 1000"
+        },
+        {
+          "description": "Edit end and leave start as it is:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...xyz -e 2000"
+        }
+      ],
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "New start coordinate (1-based)",
+          "name": "start",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "end": {
+          "char": "e",
+          "description": "New end coordinate (1-based)",
+          "name": "end",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:edit-coords",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Edit feature start and/or end coordinates",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "edit-coords.js"
+      ]
+    },
+    "feature:edit-type": {
+      "aliases": [],
+      "args": {},
+      "description": "Feature type is column 3 in gff format. It must be a valid sequence ontology\nterm although but the valifdity of the new term is not checked.",
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Feature ID to edit or \"-\" to read it from stdin",
+          "name": "feature-id",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "type": {
+          "char": "t",
+          "description": "Assign feature to this type. If unset return the current type",
+          "name": "type",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:edit-type",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Edit or view feature type",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "edit-type.js"
+      ]
+    },
+    "feature:edit": {
+      "aliases": [],
+      "args": {},
+      "description": "Edit a feature by submitting a json input with all the required attributes for\nApollo to process it. This is a very low level command which most users probably\ndo not need.\n\n Input may be a json string or a json file and it may be an array of changes.\nThis is an example input for editing feature type:\n\n {\n \"typeName\": \"TypeChange\",\n \"changedIds\": [\n \"6613f7d22c957525d631b1cc\"\n ],\n \"assembly\": \"6613f7d1360321540a11e5ed\",\n \"featureId\": \"6613f7d22c957525d631b1cc\",\n \"oldType\": \"BAC\",\n \"newType\": \"G_quartet\"\n }",
+      "examples": [
+        {
+          "description": "Editing by passing a json to stdin:",
+          "command": "echo '{\"typeName\": ... \"newType\": \"G_quartet\"}' | <%= config.bin %> <%= command.id %> -j -"
+        }
+      ],
+      "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"
+        },
+        "json-input": {
+          "char": "j",
+          "description": "Json string or json file or \"-\" to read json from stdin",
+          "name": "json-input",
+          "default": "-",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:edit",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Edit features using an appropiate json input",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "edit.js"
+      ]
+    },
+    "feature:get-id": {
+      "aliases": [],
+      "args": {},
+      "description": "Invalid identifiers or identifiers not found in the database will be silently\nignored",
+      "examples": [
+        {
+          "description": "Get features for these identifiers:",
+          "command": "<%= config.bin %> <%= command.id %> -i abc...zyz def...foo"
+        }
+      ],
+      "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"
+        },
+        "feature-id": {
+          "char": "i",
+          "description": "Retrieves feature with these IDs. Use\n\"-\" to read IDs from stdin (one per\nline)",
+          "name": "feature-id",
+          "default": [
+            "-"
+          ],
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:get-id",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get features given their identifiers",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "get-id.js"
+      ]
+    },
+    "feature:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Get features in assembly, reference sequence or genomic window",
+      "examples": [
+        {
+          "description": "Get all features in myAssembly:",
+          "command": "<%= config.bin %> <%= command.id %> -a myAssembly"
+        },
+        {
+          "description": "Get features intersecting chr1:1..1000. You can omit the assembly name if there\nare no other reference sequences named chr1:",
+          "command": "<%= config.bin %> <%= command.id %> -a myAssembly -r chr1 -s 1 -e 1000"
+        }
+      ],
+      "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": "Find input reference sequence in this assembly",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "refseq": {
+          "char": "r",
+          "description": "Reference sequence. If unset, query all sequences",
+          "name": "refseq",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "start": {
+          "char": "s",
+          "description": "Start coordinate (1-based)",
+          "name": "start",
+          "default": 1,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "end": {
+          "char": "e",
+          "description": "End coordinate",
+          "name": "end",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "get.js"
+      ]
+    },
+    "feature:import": {
+      "aliases": [],
+      "args": {},
+      "description": "By default, features are added to the existing ones.",
+      "examples": [
+        {
+          "description": "Delete features in myAssembly and then import features.gff3:",
+          "command": "<%= config.bin %> <%= command.id %> -d -i features.gff3 -a myAssembly"
+        }
+      ],
+      "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"
+        },
+        "input-file": {
+          "char": "i",
+          "description": "Input gff or gtf file",
+          "name": "input-file",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Import into this assembly name or assembly ID",
+          "name": "assembly",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "delete-existing": {
+          "char": "d",
+          "description": "Delete existing features before importing",
+          "name": "delete-existing",
+          "allowNo": false,
+          "type": "boolean"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:import",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Import features from local gff file",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "import.js"
+      ]
+    },
+    "feature:search": {
+      "aliases": [],
+      "args": {},
+      "description": "Return features matching a query string. This command searches only in:\n\n - Attribute *values* (not attribute names)\n - Source field (which in fact is stored as an attribute)\n - Feature type\n\n The search mode is:\n\n - Case insensitive\n - Match only full words, but not necessarily the full value\n - Common words are ignored. E.g. \"the\", \"with\"\n\n For example, given this feature:\n\n chr1 example SNP 10 30 0.987 . . \"someKey=Fingerprint BAC with reads\"\n\n Queries \"bac\" or \"mRNA\" return the feature. Instead these queries will NOT\nmatch:\n\n - \"someKey\"\n - \"with\"\n - \"Finger\"\n - \"chr1\"\n - \"0.987\"",
+      "examples": [
+        {
+          "description": "Search \"bac\" in these assemblies:",
+          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10 -t bac"
+        }
+      ],
+      "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"
+        },
+        "text": {
+          "char": "t",
+          "description": "Search for this text query",
+          "name": "text",
+          "required": true,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted\nsearch all assemblies",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "feature:search",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Free text search for feature in one or more assemblies",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "feature",
+        "search.js"
+      ]
+    }
+  },
+  "version": "0.1.10"
+}