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Fix blank lines in GFF crashing text-index #3747

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merged 2 commits into from Jun 7, 2023
Merged

Fix blank lines in GFF crashing text-index #3747

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de50255
Update yarn.lock
cmdcolin Jun 6, 2023
55cb088
Fix gff3 blank lines
cmdcolin Jun 6, 2023
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4 changes: 3 additions & 1 deletion products/jbrowse-cli/src/types/gff3Adapter.ts
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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
Expand Down
60 changes: 14 additions & 46 deletions website/docs/config/JBrowseRootConfig.md
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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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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<...>>>...
```