@jbrowse/plugin-alignments - npm Package Versions

2.2.0 (2022-11-04)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #3296 Add option to use OAuth "state" param in internet accounts (@garrettjstevens)
  • #3285 Use typescript version of @gmod/cram (@cmdcolin)
• core
  • #3299 Add ability to open a synteny track directly from the dotplot/linear synteny view import forms (@cmdcolin)
  • #3287 Lazy-load assemblies on demand instead of all at app startup (@cmdcolin)
  • #3279 Remove unnecessary expanded region query and small refactors (@cmdcolin)

:bug: Bug Fix

• core
  • #3309 Fix animated "Loading..." message keyframes (@cmdcolin)
  • #3306 Fix the RefNameAutocomplete displaying a stale value for chromosome names (@cmdcolin)
  • #3302 Improve rubberband zooming across elided regions (@cmdcolin)
• Other
  • #3293 Fix CRAM plotting for data files that encode insertions in uncommon way (@cmdcolin)

:memo: Documentation

• core, text-indexing
  • #3278 Auto-generate docs (@cmdcolin)

:house: Internal

• #3310 Remove CacheProvider emotion cache (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain)

2.1.7 (2022-10-20)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

</p> </details>

:bug: Bug Fix

• #3282 Fix for embedded build with webpack 4 failing with v2.1.6 (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.1.6 (2022-10-19)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | jbrowse-predefined-sessions | | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #3272 Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff (@cmdcolin)
  • #3254 Use tick labels that correspond to the overview's larger zoom level (@cmdcolin)
• core
  • #3230 Add ability to customize About dialog with callbacks and optionally hide links to data (@cmdcolin)
  • #3275 Add help dialog for feature sequence panel (@cmdcolin)
  • #3250 Handle alternate line endings (@garrettjstevens)
  • #3252 Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types (@cmdcolin)
• core, text-indexing
  • #3276 Allow using web worker RPC on embedded LGV (@cmdcolin)

:bug: Bug Fix

• core
  • #3266 Fix relative path loading of plugins (@cmdcolin)
  • #3269 Fix ability to rename session in web/desktop (@cmdcolin)
  • #3256 Fix tracks hanging in safari and polyfill for bigwig tracks (@cmdcolin)
• Other
  • #3274 Update bbi-js for bugfix on webpack 4 (@cmdcolin)
  • #3259 Fix issue with breakpoint split view using view before initialized (@cmdcolin)

:memo: Documentation

• #3255 Add more docs about color callbacks (@cmdcolin)

:house: Internal

• core
  • #3261 Fix for flaky test (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain)

2.1.5 (2022-10-03)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #3200 Use Alert component for track messages (@garrettjstevens)
  • #3229 Allow user to select local assembly to add tracks to for trackhub registry (@cmdcolin)
  • #3220 Improve error reporting on SV inspector/spreadsheet view on import form (@cmdcolin)
  • #3198 Improve error reporting on jbrowse-web start screen when user attempts to open a broken recent session (@carolinebridge-oicr)
• core
  • #3223 Allow adding session tracks to embedded react component along with disableAddTracks option if unwanted (@cmdcolin)
  • #3227 Add infrastructure for creating linear-genome-view sub-classes (@carolinebridge-oicr)
  • #3215 Add error boundary on view, track, and drawer widget (@cmdcolin)
  • #3216 Add ability to set number of bp to fetch up/down stream/inside intron in feature details (@cmdcolin)

:bug: Bug Fix

• Other
  • #3241 Fix local session failing to load copying between tabs in some cases (@cmdcolin)
  • #3234 Fix circular embedded view failing to load in v2.1.3 and v2.1.4 (@cmdcolin)
  • #3233 Fix legend being cutoff on multiwiggle tracks with wide window (@cmdcolin)
  • #3217 Fix loading tracks from connection using assembly alias (@cmdcolin)
  • #3214 Fix trackhub registry failing to load in 2.x.y versions of jbrowse (@cmdcolin)
  • #3204 Fix authentication configuration on jbrowse-desktop (@cmdcolin)
• core
  • #3231 Fix theme coloring for components that use overrides e.g. accordion summary (@garrettjstevens)

:memo: Documentation

• #3193 Add desktop specific plugin tutorial (@carolinebridge-oicr)

:house: Internal

• Other
  • #3243 Add component test for circular genome view (@cmdcolin)
  • #3242 Fix flaky test in plugins/linear-genome-view (@cmdcolin)
• core
  • #3228 Improve TypeScript for queueDialog (@garrettjstevens)
  • #3224 More typescripting of plain js files (@cmdcolin)
  • #3207 Hardcoded block width of 800px on static blocks (@cmdcolin)
  • #3197 Use "temporaryAssemblies" to store read vs ref assemblies, and allow selecting "sessionAssemblies" in dropdown (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.1.4 (2022-09-16)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

</p> </details>

:bug: Bug Fix

• #3191 Fix the UMD build of the react embedded components (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.1.3 (2022-09-15)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #3188 Add 'Open saved session' button to start screen on desktop (@cmdcolin)
  • #3187 Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table (@cmdcolin)
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
  • #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
  • #3162 Add about dialog with version number for embedded components (@cmdcolin)
  • #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
  • #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
  • #3162 Add about dialog with version number for embedded components (@cmdcolin)
  • #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
• core
  • #3180 Improve adding assemblies internally, and use the assembly displayName in more places in the UI (@garrettjstevens)
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)

:bug: Bug Fix

• core
  • #3168 Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form (@cmdcolin)
  • #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
  • #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
• Other
  • #3170 Fix drawing inverted CIGAR segments on dotplot (@cmdcolin)
  • #3170 Fix drawing inverted CIGAR segments on dotplot (@cmdcolin)

:memo: Documentation

• #3138 Documentation overhaul (@carolinebridge-oicr)
• #3138 Documentation overhaul (@carolinebridge-oicr)

:house: Internal

• Other
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3165 Use more defaults in rollup plugins (@garrettjstevens)
• core
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3164 Typescript the QuickLRU module in @jbrowse/core (@cmdcolin)
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3164 Typescript the QuickLRU module in @jbrowse/core (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

2.1.0 (2022-07-28)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | ------------------------------------ | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-hic | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• core
  • #3111 Create undo manager in jbrowse-web and jbrowse-desktop (@cmdcolin)
  • #3115 Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view (@cmdcolin)
  • #3102 Allow creating alternative "add track workflows" from within the "Add track" widget (@cmdcolin)
  • #3043 Create MultiWiggle track type, adapter, and renderers (@cmdcolin)
• Other
  • #3113 Improve SVG performance by avoiding re-render when feature is clicked (@cmdcolin)
  • #3110 Remove TSDX from plugin development tools (@garrettjstevens)
  • #3106 Add "emphasis" mode for no fill/scatterplot mode in XYPlot type renderings (@cmdcolin)

:bug: Bug Fix

• Other
  • #3109 Better support for developing plugins from within yarn 2+ workspaces (include __virtual folder in build) (@garrettjstevens)
• core
  • #3095 Add MUI exports to re-exports list (@garrettjstevens)
  • #3092 Fix use of embedded components with vite 3.0 using tsc to compile @jbrowse/core (@cmdcolin)

:memo: Documentation

• #3116 Add docs for multi-wiggle tracks (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.0.1 (2022-07-13)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• core
  • #3089 Clarify error message when adapter has no features (@garrettjstevens)
  • #3084 Show a descriptive error if an adapter doesn't provide a sequence (@garrettjstevens)
  • #3071 Add ability to mouseover/click on synteny feature polygons in the linear synteny view (@cmdcolin)
• Other
  • #3081 Add ability to toggle gridlines on the LGV (@cmdcolin)

:bug: Bug Fix

• Other
  • #3088 Fix labels being cut-off in SVG features by rendering feature labels on main thread (@cmdcolin)
  • #3085 Fix zoom to behavior being inaccurate with many displayed regions visible (@cmdcolin)
  • #3082 Fix negative strand CIGAR renderings on linear synteny view (@cmdcolin)
  • #3077 Fix crash opening multiple synteny track selectors launched from dotplot view (@cmdcolin)
• core
  • #3086 Fix pxToBp and bpToPx calculations when there are many displayed regions (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.0.0 (2022-07-07)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #3001 Draw SNPs in modifications/methylation views (@cmdcolin)
  • #3068 Allow HTML in feature tooltips, remove react-simple-code-editor (@cmdcolin)
  • #3065 Allow changing between xyplot,line,density for linear wiggle tracks and other small fixes (@cmdcolin)
• text-indexing
  • #3058 Improve bundle size and code splitting on embedded builds (v2) (@cmdcolin)
• __mocks__, core, text-indexing
  • #2949 Upgrade to MUI v5, mobx-state-tree v5, mobx-react v6, mobx-react v7 (@cmdcolin)

:bug: Bug Fix

• Other
  • #3072 Fix the display of inversions for MCScan alignments (@cmdcolin)
  • #3057 Fix export SVG crash on some BigWig tracks (@cmdcolin)
  • #3052 Fix negative value quantitative display in svg exports (@cmdcolin)
• core
  • #3064 Fix opening link in new tab by default in feature details (@cmdcolin)
  • #3053 Avoid displaying [object Object] on deeply nested data in base feature details (@cmdcolin)

:house: Internal

• #3067 Typescriptify some integration tests (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)