@apollo-annotation/cli 0.3.9 → 0.3.11
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +125 -35
- package/dist/commands/feature/add.d.ts +57 -0
- package/dist/commands/feature/add.js +323 -0
- package/dist/commands/feature/get-indexed-id.d.ts +17 -0
- package/dist/commands/feature/get-indexed-id.js +66 -0
- package/dist/test/test.js +194 -2
- package/oclif.manifest.json +303 -100
- package/package.json +4 -3
package/oclif.manifest.json
CHANGED
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@@ -236,105 +236,6 @@
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"status.js"
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]
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},
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"change:get": {
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"aliases": [],
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"args": {},
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"description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
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"flags": {
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"profile": {
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"description": "Use credentials from this profile",
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"name": "profile",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"config-file": {
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"description": "Use this config file (mostly for testing)",
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"name": "config-file",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"assembly": {
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"char": "a",
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"description": "Get changes only for these assembly names or IDs (but see description)",
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"name": "assembly",
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"hasDynamicHelp": false,
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"multiple": true,
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"type": "option"
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}
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},
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"hasDynamicHelp": false,
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"hiddenAliases": [],
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"id": "change:get",
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"pluginAlias": "@apollo-annotation/cli",
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"pluginName": "@apollo-annotation/cli",
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"pluginType": "core",
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"strict": true,
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"summary": "Get list of changes",
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"enableJsonFlag": false,
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"isESM": true,
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"relativePath": [
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"dist",
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"commands",
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"change",
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"get.js"
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]
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},
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"export:gff3": {
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"aliases": [],
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"args": {
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"assembly": {
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"description": "Export annotations for this assembly name or id",
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"name": "assembly",
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"required": true
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}
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},
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"description": "Export the annotations for an assembly to stdout as gff3",
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"examples": [
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{
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"description": "Export annotations for myAssembly:",
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"command": "<%= config.bin %> <%= command.id %> myAssembly > out.gff3"
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}
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],
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"flags": {
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"profile": {
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"description": "Use credentials from this profile",
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"name": "profile",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"config-file": {
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"description": "Use this config file (mostly for testing)",
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"name": "config-file",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"include-fasta": {
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"description": "Include fasta sequence in output",
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"name": "include-fasta",
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"allowNo": false,
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"type": "boolean"
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}
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},
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"hasDynamicHelp": false,
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"hiddenAliases": [],
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"id": "export:gff3",
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"pluginAlias": "@apollo-annotation/cli",
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"pluginName": "@apollo-annotation/cli",
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"pluginType": "core",
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"strict": true,
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"enableJsonFlag": false,
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"isESM": true,
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"relativePath": [
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"dist",
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"commands",
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"export",
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"gff3.js"
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]
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},
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"assembly:add-from-fasta": {
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"aliases": [],
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"args": {
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@@ -783,6 +684,105 @@
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"sequence.js"
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]
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},
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"change:get": {
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"aliases": [],
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"args": {},
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"description": "Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such cases you need to use the assembly ID.",
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"flags": {
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"profile": {
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"description": "Use credentials from this profile",
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"name": "profile",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"config-file": {
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"description": "Use this config file (mostly for testing)",
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"name": "config-file",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"assembly": {
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"char": "a",
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"description": "Get changes only for these assembly names or IDs (but see description)",
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"name": "assembly",
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"hasDynamicHelp": false,
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"multiple": true,
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"type": "option"
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}
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},
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"hasDynamicHelp": false,
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"hiddenAliases": [],
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"id": "change:get",
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"pluginAlias": "@apollo-annotation/cli",
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"pluginName": "@apollo-annotation/cli",
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"pluginType": "core",
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"strict": true,
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"summary": "Get list of changes",
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"enableJsonFlag": false,
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"isESM": true,
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"relativePath": [
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"dist",
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"commands",
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"change",
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"get.js"
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]
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},
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"export:gff3": {
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"aliases": [],
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"args": {
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"assembly": {
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"description": "Export annotations for this assembly name or id",
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"name": "assembly",
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"required": true
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}
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},
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"description": "Export the annotations for an assembly to stdout as gff3",
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"examples": [
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{
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"description": "Export annotations for myAssembly:",
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"command": "<%= config.bin %> <%= command.id %> myAssembly > out.gff3"
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}
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],
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"flags": {
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"profile": {
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"description": "Use credentials from this profile",
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"name": "profile",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"config-file": {
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"description": "Use this config file (mostly for testing)",
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"name": "config-file",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"include-fasta": {
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"description": "Include fasta sequence in output",
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"name": "include-fasta",
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"allowNo": false,
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"type": "boolean"
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}
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},
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"hasDynamicHelp": false,
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"hiddenAliases": [],
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"id": "export:gff3",
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"pluginAlias": "@apollo-annotation/cli",
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"pluginName": "@apollo-annotation/cli",
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"pluginType": "core",
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"strict": true,
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"enableJsonFlag": false,
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"isESM": true,
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"relativePath": [
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"dist",
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"commands",
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"export",
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"gff3.js"
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]
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},
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"feature:add-child": {
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"aliases": [],
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"args": {},
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@@ -862,6 +862,146 @@
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"add-child.js"
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]
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},
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"feature:add": {
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"aliases": [],
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"args": {
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"feature-json": {
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"description": "Inline JSON describing the feature(s) to add. Can also be provided via stdin.",
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"name": "feature-json"
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}
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},
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873
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"description": "A single simple feature can be added using the --min, --max, etc. flags.\n\nTo add multiple features, features with more details, or features with children, you can pass in JSON via argument or stdin or use the --feature-json-file options.\n",
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"examples": [
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{
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"description": "Add a single feature by specifying its location and type",
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"command": "<%= config.bin %> <%= command.id %> --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark"
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},
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{
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"description": "Add a single feature from inline JSON",
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"command": "<%= config.bin %> <%= command.id %> '{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\"}'"
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882
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},
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883
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{
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884
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"description": "Add mutilple features from stdin JSON",
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"command": "echo '[{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\"},{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":101,\"max\":200,\"type\":\"<featureType>\"}]' | <%= config.bin %> <%= command.id %>"
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886
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},
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887
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{
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888
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"description": "Add a feature with children from inline JSON",
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889
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"command": "<%= config.bin %> <%= command.id %> '{\"assembly\":\"<assemblyNameOrId>\",\"refseq\":\"<refSeqNameOrId>\",\"min\":1,\"max\":100,\"type\":\"<featureType>\",\"children\":[{\"min\":1,\"max\":50,\"type\":\"<featureType>\"}]}'"
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}
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],
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"flags": {
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"profile": {
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"description": "Use credentials from this profile",
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"name": "profile",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"config-file": {
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"description": "Use this config file (mostly for testing)",
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"name": "config-file",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"assembly": {
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"char": "a",
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"description": "Name or ID of target assembly. Not required if refseq is unique in the database",
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"name": "assembly",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"refSeq": {
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"char": "r",
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"dependsOn": [
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"min",
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"max",
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"type"
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],
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"description": "Name or ID of target reference sequence",
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"exclusive": [
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"feature-json-file"
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],
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"name": "refSeq",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"min": {
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"char": "s",
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"dependsOn": [
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"refSeq",
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"max",
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"type"
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],
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"description": "Start position in target reference sequence",
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"exclusive": [
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"feature-json-file"
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],
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"name": "min",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"max": {
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"char": "e",
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"dependsOn": [
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"refSeq",
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"min",
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"type"
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],
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"description": "End position in target reference sequence",
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"exclusive": [
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"feature-json-file"
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],
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"name": "max",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"type": {
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"char": "t",
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"dependsOn": [
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"refSeq",
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"min",
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"max"
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],
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"description": "Type of child feature",
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"exclusive": [
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"feature-json-file"
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],
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"name": "type",
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"hasDynamicHelp": false,
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"multiple": false,
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+
"type": "option"
|
|
978
|
+
},
|
|
979
|
+
"feature-json-file": {
|
|
980
|
+
"char": "F",
|
|
981
|
+
"description": "File with JSON describing the feature(s) to add",
|
|
982
|
+
"name": "feature-json-file",
|
|
983
|
+
"hasDynamicHelp": false,
|
|
984
|
+
"multiple": false,
|
|
985
|
+
"type": "option"
|
|
986
|
+
}
|
|
987
|
+
},
|
|
988
|
+
"hasDynamicHelp": false,
|
|
989
|
+
"hiddenAliases": [],
|
|
990
|
+
"id": "feature:add",
|
|
991
|
+
"pluginAlias": "@apollo-annotation/cli",
|
|
992
|
+
"pluginName": "@apollo-annotation/cli",
|
|
993
|
+
"pluginType": "core",
|
|
994
|
+
"strict": true,
|
|
995
|
+
"summary": "Add one or more features to Apollo",
|
|
996
|
+
"enableJsonFlag": false,
|
|
997
|
+
"isESM": true,
|
|
998
|
+
"relativePath": [
|
|
999
|
+
"dist",
|
|
1000
|
+
"commands",
|
|
1001
|
+
"feature",
|
|
1002
|
+
"add.js"
|
|
1003
|
+
]
|
|
1004
|
+
},
|
|
865
1005
|
"feature:check": {
|
|
866
1006
|
"aliases": [],
|
|
867
1007
|
"args": {},
|
|
@@ -1382,6 +1522,69 @@
|
|
|
1382
1522
|
"get-id.js"
|
|
1383
1523
|
]
|
|
1384
1524
|
},
|
|
1525
|
+
"feature:get-indexed-id": {
|
|
1526
|
+
"aliases": [],
|
|
1527
|
+
"args": {
|
|
1528
|
+
"id": {
|
|
1529
|
+
"description": "Indexed identifier to search for",
|
|
1530
|
+
"name": "id",
|
|
1531
|
+
"required": true
|
|
1532
|
+
}
|
|
1533
|
+
},
|
|
1534
|
+
"description": "Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file",
|
|
1535
|
+
"examples": [
|
|
1536
|
+
{
|
|
1537
|
+
"description": "Get features for this indexed identifier:",
|
|
1538
|
+
"command": "<%= config.bin %> <%= command.id %> -i abc...zyz def...foo"
|
|
1539
|
+
}
|
|
1540
|
+
],
|
|
1541
|
+
"flags": {
|
|
1542
|
+
"profile": {
|
|
1543
|
+
"description": "Use credentials from this profile",
|
|
1544
|
+
"name": "profile",
|
|
1545
|
+
"hasDynamicHelp": false,
|
|
1546
|
+
"multiple": false,
|
|
1547
|
+
"type": "option"
|
|
1548
|
+
},
|
|
1549
|
+
"config-file": {
|
|
1550
|
+
"description": "Use this config file (mostly for testing)",
|
|
1551
|
+
"name": "config-file",
|
|
1552
|
+
"hasDynamicHelp": false,
|
|
1553
|
+
"multiple": false,
|
|
1554
|
+
"type": "option"
|
|
1555
|
+
},
|
|
1556
|
+
"assembly": {
|
|
1557
|
+
"char": "a",
|
|
1558
|
+
"description": "Assembly names or IDs to search; use \"-\" to read it from stdin. If omitted search all assemblies",
|
|
1559
|
+
"name": "assembly",
|
|
1560
|
+
"hasDynamicHelp": false,
|
|
1561
|
+
"multiple": true,
|
|
1562
|
+
"type": "option"
|
|
1563
|
+
},
|
|
1564
|
+
"topLevel": {
|
|
1565
|
+
"description": "Return the top-level parent of the feature instead of the feature itself",
|
|
1566
|
+
"name": "topLevel",
|
|
1567
|
+
"allowNo": false,
|
|
1568
|
+
"type": "boolean"
|
|
1569
|
+
}
|
|
1570
|
+
},
|
|
1571
|
+
"hasDynamicHelp": false,
|
|
1572
|
+
"hiddenAliases": [],
|
|
1573
|
+
"id": "feature:get-indexed-id",
|
|
1574
|
+
"pluginAlias": "@apollo-annotation/cli",
|
|
1575
|
+
"pluginName": "@apollo-annotation/cli",
|
|
1576
|
+
"pluginType": "core",
|
|
1577
|
+
"strict": true,
|
|
1578
|
+
"summary": "Get features given an indexed identifier",
|
|
1579
|
+
"enableJsonFlag": false,
|
|
1580
|
+
"isESM": true,
|
|
1581
|
+
"relativePath": [
|
|
1582
|
+
"dist",
|
|
1583
|
+
"commands",
|
|
1584
|
+
"feature",
|
|
1585
|
+
"get-indexed-id.js"
|
|
1586
|
+
]
|
|
1587
|
+
},
|
|
1385
1588
|
"feature:get": {
|
|
1386
1589
|
"aliases": [],
|
|
1387
1590
|
"args": {},
|
|
@@ -2196,5 +2399,5 @@
|
|
|
2196
2399
|
]
|
|
2197
2400
|
}
|
|
2198
2401
|
},
|
|
2199
|
-
"version": "0.3.
|
|
2402
|
+
"version": "0.3.11"
|
|
2200
2403
|
}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@apollo-annotation/cli",
|
|
3
|
-
"version": "0.3.
|
|
3
|
+
"version": "0.3.11",
|
|
4
4
|
"description": "Command line interface for the Apollo annotation server",
|
|
5
5
|
"repository": {
|
|
6
6
|
"type": "git",
|
|
@@ -89,8 +89,8 @@
|
|
|
89
89
|
"yaml": "^2.3.4"
|
|
90
90
|
},
|
|
91
91
|
"devDependencies": {
|
|
92
|
-
"@apollo-annotation/mst": "^0.3.
|
|
93
|
-
"@apollo-annotation/shared": "^0.3.
|
|
92
|
+
"@apollo-annotation/mst": "^0.3.11",
|
|
93
|
+
"@apollo-annotation/shared": "^0.3.11",
|
|
94
94
|
"@istanbuljs/esm-loader-hook": "^0.2.0",
|
|
95
95
|
"@istanbuljs/nyc-config-typescript": "^1.0.2",
|
|
96
96
|
"@oclif/test": "^3.1.3",
|
|
@@ -103,6 +103,7 @@
|
|
|
103
103
|
"babel-plugin-istanbul": "^6.1.1",
|
|
104
104
|
"cross-spawn": "^7.0.3",
|
|
105
105
|
"mocha": "^10.2.0",
|
|
106
|
+
"mongodb": "^4.7.0",
|
|
106
107
|
"nyc": "^15.1.0",
|
|
107
108
|
"oclif": "^4.4.2",
|
|
108
109
|
"prettier": "^3.3.2",
|