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Fix gff3 blank lines
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@cmdcolin
cmdcolin committed Jun 7, 2023
1 parent de50255 commit 55cb088
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Showing 4 changed files with 64 additions and 97 deletions.
4 changes: 3 additions & 1 deletion products/jbrowse-cli/src/types/gff3Adapter.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,9 @@ export async function* indexGff3({
})

for await (const line of rl) {
if (line.startsWith('#')) {
if (!line.trim()) {
continue
} else if (line.startsWith('#')) {
continue
} else if (line.startsWith('>')) {
break
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60 changes: 14 additions & 46 deletions website/docs/config/JBrowseRootConfig.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,30 +2,26 @@
id: jbrowserootconfig
title: JBrowseRootConfig
---
Note: this document is automatically generated from configuration objects in
our source code. See [Config guide](/docs/config_guide) for more info

Note: this document is automatically generated from configuration objects in our
source code. See [Config guide](/docs/config_guide) for more info

### Source file

[packages/app-core/src/JBrowseConfig/index.ts](https://github.com/GMOD/jbrowse-components/blob/main/packages/app-core/src/JBrowseConfig/index.ts)

configuration in a config.json/file.jbrowse



### JBrowseRootConfig - Slots
#### slot: configuration.rpc


#### slot: configuration.rpc

```js
rpc: RpcManager.configSchema
```

#### slot: configuration.highResolutionScaling



```js
highResolutionScaling: {
type: 'number',
Expand All @@ -35,8 +31,6 @@ highResolutionScaling: {

#### slot: configuration.formatDetails.feature



```js
feature: {
type: 'frozen',
Expand All @@ -48,8 +42,6 @@ feature: {

#### slot: configuration.formatDetails.subfeatures



```js
subfeatures: {
type: 'frozen',
Expand All @@ -61,8 +53,6 @@ subfeatures: {

#### slot: configuration.formatDetails.depth



```js
depth: {
type: 'number',
Expand All @@ -73,8 +63,6 @@ depth: {

#### slot: configuration.formatAbout.config



```js
config: {
type: 'frozen',
Expand All @@ -86,8 +74,6 @@ config: {

#### slot: configuration.formatAbout.hideUris



```js
hideUris: {
type: 'boolean',
Expand All @@ -97,8 +83,6 @@ hideUris: {

#### slot: configuration.disableAnalytics



```js
disableAnalytics: {
type: 'boolean',
Expand All @@ -108,8 +92,6 @@ disableAnalytics: {

#### slot: configuration.theme



```js
theme: {
type: 'frozen',
Expand All @@ -119,16 +101,12 @@ theme: {

#### slot: configuration.extraThemes



```js
extraThemes: { type: 'frozen', defaultValue: {} }
```

#### slot: configuration.logoPath



```js
logoPath: {
type: 'fileLocation',
Expand All @@ -139,6 +117,7 @@ logoPath: {
#### slot: plugins

defines plugins of the format

```typescript
type PluginDefinition=
{ umdUrl: string, name:string } |
Expand All @@ -163,8 +142,8 @@ assemblies: types.array(assemblyConfigSchema)
#### slot: tracks
track configuration is an array of track config schemas. multiple
instances of a track can exist that use the same configuration
track configuration is an array of track config schemas. multiple instances of a
track can exist that use the same configuration
```js
tracks: types.array(pluginManager.pluggableConfigSchemaType('track'))
Expand All @@ -176,39 +155,28 @@ configuration for internet accounts, see InternetAccounts
```js
internetAccounts: types.array(
pluginManager.pluggableConfigSchemaType('internet account'),
)
pluginManager.pluggableConfigSchemaType('internet account'),
)
```
#### slot: aggregateTextSearchAdapters
```js
aggregateTextSearchAdapters: types.array(
pluginManager.pluggableConfigSchemaType('text search adapter'),
)
pluginManager.pluggableConfigSchemaType('text search adapter'),
)
```
#### slot: connections
```js
connections: types.array(
pluginManager.pluggableConfigSchemaType('connection'),
)
connections: types.array(pluginManager.pluggableConfigSchemaType('connection'))
```
#### slot: defaultSession
```js
defaultSession: types.optional(types.frozen(), {
name: `New Session`,
})
name: `New Session`,
})
```
21 changes: 4 additions & 17 deletions website/docs/models/DesktopSessionTrackMenuMixin.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,32 +4,19 @@ title: DesktopSessionTrackMenuMixin
---

Note: this document is automatically generated from mobx-state-tree objects in
our source code. See [Core concepts and intro to pluggable
elements](/docs/developer_guide/) for more info
our source code. See
[Core concepts and intro to pluggable elements](/docs/developer_guide/) for more
info

### Source file

[products/jbrowse-desktop/src/sessionModel/TrackMenu.ts](https://github.com/GMOD/jbrowse-components/blob/main/products/jbrowse-desktop/src/sessionModel/TrackMenu.ts)









### DesktopSessionTrackMenuMixin - Methods
#### method: getTrackActionMenuItems


#### method: getTrackActionMenuItems

```js
// type signature
getTrackActionMenuItems: (trackConfig: { [x: string]: any; } & NonEmptyObject & { setSubschema(slotName: string, data: unknown): any; } & IStateTreeNode<ConfigurationSchemaType<{ name: { description: string; type: string; defaultValue: string; }; ... 8 more ...; formatAbout: ConfigurationSchemaType<...>; }, ConfigurationSchemaOptions<...>>>...
```
76 changes: 43 additions & 33 deletions yarn.lock
View file
Original file line number Diff line number Diff line change
Expand Up @@ -516,9 +516,9 @@
"@babel/helper-plugin-utils" "^7.18.6"

"@babel/plugin-proposal-private-property-in-object@^7.21.0":
version "7.21.10"
resolved "https://registry.yarnpkg.com/@babel/plugin-proposal-private-property-in-object/-/plugin-proposal-private-property-in-object-7.21.10.tgz#861ab9c7d152291c47d27838867f27c560f562c4"
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version "7.21.11"
resolved "https://registry.yarnpkg.com/@babel/plugin-proposal-private-property-in-object/-/plugin-proposal-private-property-in-object-7.21.11.tgz#69d597086b6760c4126525cfa154f34631ff272c"
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dependencies:
"@babel/helper-annotate-as-pure" "^7.18.6"
"@babel/helper-create-class-features-plugin" "^7.21.0"
Expand Down Expand Up @@ -2949,10 +2949,10 @@
dependencies:
semver "^7.3.5"

"@npmcli/git@^4.0.0":
version "4.0.4"
resolved "https://registry.yarnpkg.com/@npmcli/git/-/git-4.0.4.tgz#cdf74f21b1d440c0756fb28159d935129d9daa33"
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"@npmcli/git@^4.0.0", "@npmcli/git@^4.1.0":
version "4.1.0"
resolved "https://registry.yarnpkg.com/@npmcli/git/-/git-4.1.0.tgz#ab0ad3fd82bc4d8c1351b6c62f0fa56e8fe6afa6"
integrity sha512-9hwoB3gStVfa0N31ymBmrX+GuDGdVA/QWShZVqE0HK2Af+7QGGrCTbZia/SW0ImUTjTne7SP91qxDmtXvDHRPQ==
dependencies:
"@npmcli/promise-spawn" "^6.0.0"
lru-cache "^7.4.4"
Expand Down Expand Up @@ -3023,14 +3023,16 @@
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"@npmcli/package-json@^3.0.0":
version "3.1.0"
resolved "https://registry.yarnpkg.com/@npmcli/package-json/-/package-json-3.1.0.tgz#d9eb34083be4275520f3844d17fc74926d47cae1"
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version "3.1.1"
resolved "https://registry.yarnpkg.com/@npmcli/package-json/-/package-json-3.1.1.tgz#5628332aac90fa1b4d6f98e03988c5958b35e0c5"
integrity sha512-+UW0UWOYFKCkvszLoTwrYGrjNrT8tI5Ckeb/h+Z1y1fsNJEctl7HmerA5j2FgmoqFaLI2gsA1X9KgMFqx/bRmA==
dependencies:
"@npmcli/git" "^4.1.0"
glob "^10.2.2"
json-parse-even-better-errors "^3.0.0"
normalize-package-data "^5.0.0"
npm-normalize-package-bin "^3.0.1"
proc-log "^3.0.0"

"@npmcli/promise-spawn@^3.0.0":
version "3.0.0"
Expand Down Expand Up @@ -3310,11 +3312,9 @@
fancy-test "^1.4.10"

"@octokit/auth-token@^3.0.0":
version "3.0.3"
resolved "https://registry.yarnpkg.com/@octokit/auth-token/-/auth-token-3.0.3.tgz#ce7e48a3166731f26068d7a7a7996b5da58cbe0c"
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dependencies:
"@octokit/types" "^9.0.0"
version "3.0.4"
resolved "https://registry.yarnpkg.com/@octokit/auth-token/-/auth-token-3.0.4.tgz#70e941ba742bdd2b49bdb7393e821dea8520a3db"
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"@octokit/core@^4.0.0":
version "4.2.1"
Expand Down Expand Up @@ -3519,6 +3519,15 @@
resolved "https://registry.yarnpkg.com/@sigstore/protobuf-specs/-/protobuf-specs-0.1.0.tgz#957cb64ea2f5ce527cc9cf02a096baeb0d2b99b4"
integrity sha512-a31EnjuIDSX8IXBUib3cYLDRlPMU36AWX4xS8ysLaNu4ZzUesDiPt83pgrW2X1YLMe5L2HbDyaKK5BrL4cNKaQ==

"@sigstore/tuf@^1.0.0":
version "1.0.0"
resolved "https://registry.yarnpkg.com/@sigstore/tuf/-/tuf-1.0.0.tgz#13b69323e7bf8de458cd6c952c57acd1169772a5"
integrity sha512-bLzi9GeZgMCvjJeLUIfs8LJYCxrPRA8IXQkzUtaFKKVPTz0mucRyqFcV2U20yg9K+kYAD0YSitzGfRZCFLjdHQ==
dependencies:
"@sigstore/protobuf-specs" "^0.1.0"
make-fetch-happen "^11.0.1"
tuf-js "^1.1.3"

"@sinclair/typebox@^0.24.1":
version "0.24.51"
resolved "https://registry.yarnpkg.com/@sinclair/typebox/-/typebox-0.24.51.tgz#645f33fe4e02defe26f2f5c0410e1c094eac7f5f"
Expand Down Expand Up @@ -8952,9 +8961,9 @@ electron-publish@23.6.0:
mime "^2.5.2"

electron-to-chromium@^1.4.411:
version "1.4.420"
resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.420.tgz#21d4b55e9deef16cdbf009557fb2fe8f96798248"
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version "1.4.422"
resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.422.tgz#b04d0a209889f46858a4ab05f737fb81b99fec91"
integrity sha512-OQMid0IRbJv27BhlPiBK8CfGzjeq4ZCBSmpwNi1abyS8w17/BajOUu7hBI49ptDTBCz9NRFbORhWvt41dF7dwg==

electron-updater@^5.0.1:
version "5.3.0"
Expand Down Expand Up @@ -10628,9 +10637,9 @@ glob@7.1.6:
path-is-absolute "^1.0.0"

glob@^10.2.2, glob@^10.2.5:
version "10.2.6"
resolved "https://registry.yarnpkg.com/glob/-/glob-10.2.6.tgz#1e27edbb3bbac055cb97113e27a066c100a4e5e1"
integrity sha512-U/rnDpXJGF414QQQZv5uVsabTVxMSwzS5CH0p3DRCIV6ownl4f7PzGnkGmvlum2wB+9RlJWJZ6ACU1INnBqiPA==
version "10.2.7"
resolved "https://registry.yarnpkg.com/glob/-/glob-10.2.7.tgz#9dd2828cd5bc7bd861e7738d91e7113dda41d7d8"
integrity sha512-jTKehsravOJo8IJxUGfZILnkvVJM/MOfHRs8QcXolVef2zNI9Tqyy5+SeuOAZd3upViEZQLyFpQhYiHLrMUNmA==
dependencies:
foreground-child "^3.1.0"
jackspeak "^2.0.3"
Expand Down Expand Up @@ -11018,9 +11027,9 @@ html-encoding-sniffer@^3.0.0:
whatwg-encoding "^2.0.0"

html-entities@^2.1.0, html-entities@^2.3.2:
version "2.3.4"
resolved "https://registry.yarnpkg.com/html-entities/-/html-entities-2.3.4.tgz#c65db1302652a0a2986f216ef911df65015dc1ac"
integrity sha512-TtiHkpRBqP40OzizVWjwBPBsiqchEZxAg/nys6D6lIpdoVLo7sWZ/5Sf/s4UaBHQ6pzUzEr3NiItvEoO46sPtQ==
version "2.3.5"
resolved "https://registry.yarnpkg.com/html-entities/-/html-entities-2.3.5.tgz#9f117bf6a5962efc31e094f6c6dad3cf3b95e33e"
integrity sha512-72TJlcMkYsEJASa/3HnX7VT59htM7iSHbH59NSZbtc+22Ap0Txnlx91sfeB+/A7wNZg7UxtZdhAW4y+/jimrdg==

html-escaper@^2.0.0:
version "2.0.2"
Expand Down Expand Up @@ -14251,9 +14260,9 @@ node-dir@^0.1.10, node-dir@^0.1.17:
minimatch "^3.0.2"

node-fetch-native@^1.0.2:
version "1.1.1"
resolved "https://registry.yarnpkg.com/node-fetch-native/-/node-fetch-native-1.1.1.tgz#b8977dd7fe6c5599e417301ed3987bca787d3d6f"
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version "1.2.0"
resolved "https://registry.yarnpkg.com/node-fetch-native/-/node-fetch-native-1.2.0.tgz#13ec6df98f33168958dbfb6945f10aedf42e7ea8"
integrity sha512-5IAMBTl9p6PaAjYCnMv5FmqIF6GcZnawAVnzaCG0rX2aYZJ4CxEkZNtVPuTRug7fL7wyM5BQYTlAzcyMPi6oTQ==

node-fetch@2.6.7:
version "2.6.7"
Expand Down Expand Up @@ -16511,9 +16520,9 @@ react-fast-compare@^3.0.1:
integrity sha512-nsO+KSNgo1SbJqJEYRE9ERzo7YtYbou/OqjSQKxV7jcKox7+usiUVZOAC+XnDOABXggQTno0Y1CpVnuWEc1boQ==

react-inspector@^6.0.0:
version "6.0.1"
resolved "https://registry.yarnpkg.com/react-inspector/-/react-inspector-6.0.1.tgz#1a37f0165d9df81ee804d63259eaaeabe841287d"
integrity sha512-cxKSeFTf7jpSSVddm66sKdolG90qURAX3g1roTeaN6x0YEbtWc8JpmFN9+yIqLNH2uEkYerWLtJZIXRIFuBKrg==
version "6.0.2"
resolved "https://registry.yarnpkg.com/react-inspector/-/react-inspector-6.0.2.tgz#aa3028803550cb6dbd7344816d5c80bf39d07e9d"
integrity sha512-x+b7LxhmHXjHoU/VrFAzw5iutsILRoYyDq97EDYdFpPLcvqtEzk4ZSZSQjnFPbr5T57tLXnHcqFYoN1pI6u8uQ==

react-is@18.1.0:
version "18.1.0"
Expand Down Expand Up @@ -17574,11 +17583,12 @@ signal-exit@^4.0.1:
integrity sha512-MY2/qGx4enyjprQnFaZsHib3Yadh3IXyV2C321GY0pjGfVBu4un0uDJkwgdxqO+Rdx8JMT8IfJIRwbYVz3Ob3Q==

sigstore@^1.0.0, sigstore@^1.3.0, sigstore@^1.4.0:
version "1.5.2"
resolved "https://registry.yarnpkg.com/sigstore/-/sigstore-1.5.2.tgz#8d4c2a549341211cb08c687999843edc48c1a94c"
integrity sha512-X95v6xAAooVpn7PaB94TDmFeSO5SBfCtB1R23fvzr36WTfjtkiiyOeei979nbTjc8nzh6FSLeltQZuODsm1EjQ==
version "1.6.0"
resolved "https://registry.yarnpkg.com/sigstore/-/sigstore-1.6.0.tgz#887a4007c6ee83f3ef3fd844be1a0840e849c301"
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dependencies:
"@sigstore/protobuf-specs" "^0.1.0"
"@sigstore/tuf" "^1.0.0"
make-fetch-happen "^11.0.1"
tuf-js "^1.1.3"

Expand Down

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