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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| title: v2.1.3 Release | ||
| date: 2022-09-15 18:53:47 | ||
| tags: ['release', 'jbrowse 2'] | ||
| --- | ||
|
|
||
| This release includes a quality-of-life improvement for users plotting synteny | ||
| with CIGAR strings. Before this version, the x-axis in the dotplot was assumed | ||
| to be target sequence (and similarly, the top row in the linear synteny view | ||
| was assumed to be the target sequence). But now, target can be either x- or | ||
| y-axis in dotplot, and top or bottom in linear synteny views, removing the need | ||
| for the user to care as much about query-vs-target ordering. | ||
|
|
||
| This release also includes several fixes for the the behavior of text searching | ||
| in the linear genome view, a new button to open a .jbrowse file directly from | ||
| the start screen on jbrowse-desktop, and an important bugfix to plotting | ||
| inverted alignments on dotplots that affected versions v2.1.0-v2.1.2. | ||
|
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||
| Enjoy! | ||
|
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||
| ## Downloads | ||
|
|
||
| - [v2.1.3](https://github.com/GMOD/jbrowse-components/releases/tag/v2.1.3) | ||
|
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| To install JBrowse 2 for the web, you can download the link above, or you can | ||
| use the JBrowse CLI to automatically download the latest version. See the | ||
| [JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more | ||
| details. | ||
|
|
||
| See "Packages in this release" in the changelog for links to packages published | ||
| on NPM. | ||
|
|
||
| ## 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](https://github.com/GMOD/jbrowse-components/pull/3188) Add 'Open saved session' button to start screen on desktop ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3187](https://github.com/GMOD/jbrowse-components/pull/3187) Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability for CLI to recognize plaintext BED files ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about dialog with version number for embedded components ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user to wait before re-launching app on desktop update ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3178](https://github.com/GMOD/jbrowse-components/pull/3178) Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3173](https://github.com/GMOD/jbrowse-components/pull/3173) Add ability for CLI to recognize plaintext BED files ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3162](https://github.com/GMOD/jbrowse-components/pull/3162) Add about dialog with version number for embedded components ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3163](https://github.com/GMOD/jbrowse-components/pull/3163) Note for user to wait before re-launching app on desktop update ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - `core` | ||
| - [#3180](https://github.com/GMOD/jbrowse-components/pull/3180) Improve adding assemblies internally, and use the assembly displayName in more places in the UI ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
|
|
||
| #### :bug: Bug Fix | ||
|
|
||
| - `core` | ||
| - [#3168](https://github.com/GMOD/jbrowse-components/pull/3168) Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead state tree node" error by creating snapshots of parent region for block calculations ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3182](https://github.com/GMOD/jbrowse-components/pull/3182) Fix "dead state tree node" error by creating snapshots of parent region for block calculations ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - Other | ||
| - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing inverted CIGAR segments on dotplot ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3170](https://github.com/GMOD/jbrowse-components/pull/3170) Fix drawing inverted CIGAR segments on dotplot ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
|
||
| #### :memo: Documentation | ||
|
|
||
| - [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) | ||
| - [#3138](https://github.com/GMOD/jbrowse-components/pull/3138) Documentation overhaul ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) | ||
|
|
||
| #### :house: Internal | ||
|
|
||
| - Other | ||
| - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3179](https://github.com/GMOD/jbrowse-components/pull/3179) Add extendSession extension point to web and desktop ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3165](https://github.com/GMOD/jbrowse-components/pull/3165) Use more defaults in rollup plugins ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - `core` | ||
| - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3183](https://github.com/GMOD/jbrowse-components/pull/3183) Make pluginManager param to getFetcher optional ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3164](https://github.com/GMOD/jbrowse-components/pull/3164) Typescript the QuickLRU module in @jbrowse/core ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
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||
| #### Committers: 3 | ||
|
|
||
| - Caroline Bridge ([@carolinebridge-oicr](https://github.com/carolinebridge-oicr)) | ||
| - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) |
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