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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| title: v2.2.0 Release | ||
| date: 2022-11-04 19:36:44 | ||
| tags: ['release', 'jbrowse 2'] | ||
| --- | ||
|
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||
| This release includes several important improvements including | ||
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| - Lazily loading assembly refNames: previously when you had multiple assemblies | ||
| in your config, it would load all their refNames at browser startup. Now, it | ||
| only fetches refNames when you request to use an assembly. | ||
| - Simplified "synteny track selector" on the dotplot and synteny import forms | ||
| - Improved documentation! The entire jbrowse 2 documentation has been | ||
| overhauled, and the monolithic user guide, config guide, and developer guide | ||
| pages have been split into smaller pages. We also now auto-generate | ||
| documentation on our config and state tree models, and have a search bar | ||
| - Improved speed on alignments tracks: a small optimization was made for | ||
| alignments tracks that can improve performance on alignments tracks by 30% or | ||
| so especially on short reads | ||
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|  | ||
| Figure showing improved speed on short read alignments of the refactor (this | ||
| release) vs main (which was v2.1.7) | ||
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| Note that the changes to allow lazy loading assemblies may have somewhat | ||
| changed the "contract", so if your code is using the assemblyManager directly | ||
| in any places, please be aware of this change. Proper usage of the | ||
| assemblyManager API uses either | ||
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|
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| 1. use assemblyManager.get(assemblyName) which can return undefined initially, | ||
| but then this initiates the lazy load and can be caught by reactivity of | ||
| wrapping your components in observers | ||
| 2. use assemblyManager.waitForAssembly(assemblyName) function, which is | ||
| asynchronous but returns a promise. this avoids the initial return undefined | ||
| behavior | ||
| 3. avoid directly accessing e.g. assemblyManager.assemblies | ||
|
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| ## Downloads | ||
|
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||
| - [v2.2.0](https://github.com/GMOD/jbrowse-components/releases/tag/v2.2.0) | ||
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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. | ||
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| See "Packages in this release" in the changelog for links to packages published | ||
| on NPM. | ||
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| ## 2.2.0 (2022-11-04) | ||
|
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| <details><summary>Packages in this release</summary> | ||
| <p> | ||
|
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| | 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 | | | ||
|
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| </p> | ||
| </details> | ||
|
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||
| #### :rocket: Enhancement | ||
|
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| - Other | ||
| - [#3296](https://github.com/GMOD/jbrowse-components/pull/3296) Add option to use OAuth "state" param in internet accounts ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3285](https://github.com/GMOD/jbrowse-components/pull/3285) Use typescript version of @gmod/cram ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - `core` | ||
| - [#3299](https://github.com/GMOD/jbrowse-components/pull/3299) Add ability to open a synteny track directly from the dotplot/linear synteny view import forms ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3287](https://github.com/GMOD/jbrowse-components/pull/3287) Lazy-load assemblies on demand instead of all at app startup ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3279](https://github.com/GMOD/jbrowse-components/pull/3279) Remove unnecessary expanded region query and small refactors ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
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| #### :bug: Bug Fix | ||
|
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| - `core` | ||
| - [#3309](https://github.com/GMOD/jbrowse-components/pull/3309) Fix animated "Loading..." message keyframes ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3306](https://github.com/GMOD/jbrowse-components/pull/3306) Fix the RefNameAutocomplete displaying a stale value for chromosome names ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3302](https://github.com/GMOD/jbrowse-components/pull/3302) Improve rubberband zooming across elided regions ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - Other | ||
| - [#3293](https://github.com/GMOD/jbrowse-components/pull/3293) Fix CRAM plotting for data files that encode insertions in uncommon way ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
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| #### :memo: Documentation | ||
|
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| - `core`, `text-indexing` | ||
| - [#3278](https://github.com/GMOD/jbrowse-components/pull/3278) Auto-generate docs ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
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| #### :house: Internal | ||
|
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| - [#3310](https://github.com/GMOD/jbrowse-components/pull/3310) Remove CacheProvider emotion cache ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
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| #### Committers: 3 | ||
|
|
||
| - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - Scott Cain ([@scottcain](https://github.com/scottcain)) |
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