@jbrowse/cli - npm Package Versions

2.5.0 (2023-05-04)

<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-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-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @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-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @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
  • #3675 Use react-popper for tooltips in DotplotView (@cmdcolin)
  • #3637 Fix renderDelay not being applied to dynamicBlocks (@cmdcolin)
• core
  • #3677 Adjust RefNameAutocomplete width calculation to avoid ellipses (@cmdcolin)
  • #3660 Bump x-data-grid dependency, refactors for BaseFeatureDetails, add GridToolbar (@cmdcolin)
  • #3626 Update to mui x-data-grid 6 (@cmdcolin)

:bug: Bug Fix

• core
  • #3681 Guard against undefined in CoreGetFeatureDetails (@cmdcolin)
  • #3662 Fix empty feature sequence on top-level gene feature (@cmdcolin)
  • #3666 Fix text boxes being too small in Dialog boxes (@cmdcolin)
  • #3642 Fix error handling of feature detail formatter jexl callbacks (@cmdcolin)
  • #3621 Update plugin rollup polyfill package (@garrettjstevens)
  • #3620 Fix potential crashes where alignment SEQ field may be empty, simplify some display model code (@cmdcolin)
• Other
  • #3670 Only double-click zoom if not clicking on feature (@cmdcolin)
  • #3652 Fix text being invisible on overview scalebar when cytobands shown (@cmdcolin)
  • #3632 Fix mouse click-and-drag behavior in the alternative "cursor mode" for the dotplot view (@cmdcolin)
  • #3625 Fix UCSC trackhub assembly aliases matching (@andrzejgrzelak)
• __mocks__, core
  • #3630 Fix flakiness of connection test (@cmdcolin)

:memo: Documentation

• Other
  • #3676 Refactor circular genome view storybook (@cmdcolin)
  • #3671 Fix website documentation sidebar on browsers with prefers-reduced-motion (@cmdcolin)
  • #3654 Add some docs for configuring defaultSession (@cmdcolin)
• core
  • #3646 Refactor linear genome view storybook (@cmdcolin)

:house: Internal

• core
  • #3647 Refactoring navToMultiple, navToLocString, and related (@cmdcolin)
  • #3629 Typescript checking for config slot names (@rbuels)
  • #3618 Rename APIs for feature density stats and quantitative stats (@cmdcolin)
  • #3615 Add check for default export to plugin loader (@rbuels)

Committers: 4

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)
• @andrzejgrzelak

2.4.2 (2023-03-27)

<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-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-hic | | | @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-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/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
  • #3604 Alignments tags description in feature details on mouseover (@cmdcolin)
• Other
  • #3586 Add authorization(internetAccount) support for Trix index files (@andrzejgrzelak)

:bug: Bug Fix

• Other
  • #3610 Avoid cutting off import form of spreadsheet view, fix overflowed text in table header (@cmdcolin)
  • #3600 Fix using the force load button after a stats timeout (@cmdcolin)
  • #3592 Fix shading on synteny features after mouseout (@cmdcolin)
• __mocks__, core
  • #3608 Fix subfeatures formatter not being applied to feature detail panel (@cmdcolin)
  • #3607 Avoid "ResizeObserver" loop warning during development (@cmdcolin)
• core
  • #3593 Fix gene without subfeatures not being displayed in sequence feature details (@cmdcolin)

:house: Internal

• #3611 Use local data instead of remote data for LGV component test (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• @andrzejgrzelak

2.4.1 (2023-03-14)

<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-authentication | https://www.npmjs.com/package/@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-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-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
  • #3534 Improve visibility of SNPs on alignments track (@cmdcolin)
  • #3561 Add scroll zoom, d-pad, and more click+drag options to dotplot (@cmdcolin)
• Other
  • #3574 Add ability to load all built-in synteny data sources from @jbrowse/cli (@cmdcolin)
  • #3564 Use double-click to zoom in on particular offset in LGV, and make ctrl+scroll also zoom in on particular offset (@cmdcolin)

:bug: Bug Fix

• #3578 Fix selected synteny feature getting unselected after scroll (@cmdcolin)
• #3566 Fix use of "show all regions with data" feature in SV inspector with TRA entries (with CHR2 from INFO) (@cmdcolin)
• #3558 Fix visual effect from using the overview scalebar click and dragging backwards (@cmdcolin)
• #3556 Fix infinite loading state when no synteny features are visible in synteny view (@cmdcolin)
• #3551 Fix bad layout on tabix tracks that have Unicode characters (@cmdcolin)
• #3548 Fix upper case querying of jbrowse 1 text search store (@cmdcolin)
• #3545 Fix issue where clearing search box on LGV import form turns search box into loading bar (@cmdcolin)

:memo: Documentation

• #3571 Fixing link to PAG 2023 tutorial (@scottcain)

:house: Internal

• Other
  • #3567 Update github actions workflows to newer versions (@cmdcolin)
• __mocks__, core, text-indexing
  • #3557 Add additional lint rules from typescript-eslint and eslint-plugin-unicorn (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Scott Cain (@scottcain)

2.4.0 (2023-02-24)

<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 | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @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-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-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @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
  • #3527 Breakpoint split view SVG export (@cmdcolin)
  • #3510 Allow configuring default display height (@cmdcolin)
• core
  • #3513 Add ability to open refNameAliases+cytobands in "Open sequence" start screen on desktop (@cmdcolin)
  • #3512 SVG export of linear synteny view, dotplot, and circular views (@cmdcolin)
  • #3467 Create dark theme and allow user to toggle different themes from preferences dialog (@cmdcolin)

:bug: Bug Fix

• #3525 Fix missing grid ticks in dotplot (@cmdcolin)
• #3524 Fix loading session shares that have a plus sign in the sessionId (@cmdcolin)

:memo: Documentation

• #3532 Check website links in CI (@cmdcolin)
• #3507 Fix mygene.info demo track (@cmdcolin)

Committers: 2

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

2.3.4 (2023-02-01)

<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-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @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/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
  • #3494 Use transitionDuration 0 as defaultProp in theme for both popovers and menus (@cmdcolin)
  • #3488 Render HTML in faceted track selector for track data/metadata (@cmdcolin)
  • #3483 Add anchorOrigin/transformOrigin to default menu component (@cmdcolin)
  • #3470 Variant sample grid auto-size columns and resizer (@cmdcolin)
• Other
  • #3304 Faceted/data grid style track selector (@cmdcolin)
  • #3477 Larger margins to add track workflow to visually clarify next button behavior (@cmdcolin)
  • #3475 Bypass plugins.json download if unneeded during app startup (@cmdcolin)
  • #3458 Improve auto-update of sequence track height when toggling forward/reverse/translation settings (@cmdcolin)

:bug: Bug Fix

• core
  • #3482 Fix loading external plugins in embedded linear-genome-view demo (@cmdcolin)
• Other
  • #3457 Fix synteny view not drawing after horizontal flip in v2.3.3 (@cmdcolin)
  • #3459 Booleanize localstorage settings from older versions of LGV to avoid crash (@cmdcolin)

:memo: Documentation

• #3487 Storybook 7 (@cmdcolin)
• #3464 Add source file to config/state model docs (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.3.3 (2023-01-11)

<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-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-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @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-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-text-indexing | | | @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
  • #3440 "Show all regions" for dotplot and synteny views and refactor synteny rendering RPC to optimize scrolling (@cmdcolin)

:bug: Bug Fix

• Other
  • #3451 Fix auto-updates on desktop not working since v2.2.2 (@cmdcolin)
• core
  • #3428 Add missing dependencies to embedded component package.json's (@cmdcolin)

:memo: Documentation

• #3448 Typescriptify some docusaurus website code (@cmdcolin)
• #3444 Human vs mouse synteny demo (@cmdcolin)

:house: Internal

• core
  • #3445 Typescriptify more tests (@cmdcolin)
  • #3443 Restore console mocks after running (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.3.2 (2022-12-20)

<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-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-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @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

• core
  • #3422 Auto-adjust height of reference sequence track to current settings (@cmdcolin)
• Other
  • #3421 Add ability to revcomp sequence in the "Get sequence" dialog (@cmdcolin)
  • #3413 Add a "base" set of tracks and assemblies for the embedded demos (@cmdcolin)

:bug: Bug Fix

• #3419 Fix rendering base-level alignments on synteny visualizations, especially in inverted regions (@cmdcolin)
• #3416 Fix rendering alignment arcs on files that need refname renaming and add jitter setting (@cmdcolin)
• #3415 Fix circular view being rendered as a blank area if tab is opened in the background (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

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

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @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 |

</p> </details>

2.3.0 (2022-12-15)

<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-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-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @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-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-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
  • #3403 Reduce overplotting on dotplot grid lines and other misc improvements (@cmdcolin)
  • #3381 Add method for cache busting requests to the config file in jbrowse-web (@cmdcolin)
  • #3384 Add method to more easily create compact view of alignments (@cmdcolin)
• core
  • #3391 Allow arc display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag (@cmdcolin)
  • #3387 Small UI tweaks for add track workflow (@cmdcolin)
  • #3358 Create new "arc" display type to show long range connections between paired-end and split-reads (@cmdcolin)
• text-indexing
  • #3385 Optimize prefix size for text indexing automatically (@cmdcolin)

:bug: Bug Fix

• Other
  • #3407 Remove trackhub registry plugin from core plugins, moved to plugin store (@cmdcolin)
  • #3406 Fix loading connection tracks from connections that don't specify assemblyNames in config (@cmdcolin)
  • #3390 Fix positioning within large alignments for query->target LGV synteny navigation (@cmdcolin)
  • #3388 Fix search result that matches synonyms that matches multiple locations (@cmdcolin)
• core
  • #3404 Fix double-render of some synteny features (@cmdcolin)
  • #3401 Remove y-scalebar rendering placeholder values in blank and loading states (@cmdcolin)
  • #3389 Fix issue where snackbar would not show up when same error message is triggered multiple times (@cmdcolin)

:memo: Documentation

• core
  • #3396 Use prettier to word wrap markdown prose (@cmdcolin)
• Other
  • #3383 Add note to user guide about variant callers that can be used for SV inspector (@cmdcolin)

:house: Internal

• __mocks__, core, text-indexing
  • #3400 Reduce peerDependency warnings from installing dev environment (@cmdcolin)
• core
  • #3394 Simplify RPC watchWorker (@cmdcolin)
  • #3386 Fix warning when rendering circular chord displays with web worker RPC (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.2.2 (2022-12-06)

<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-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-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @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
  • #3350 Retain feature labels in compact display mode for SVG features, and allow turning off keeping feature description without feature label (@cmdcolin)
  • #3357 Allow holding shift key to create rubberband selection on LGV (@cmdcolin)
  • #3363 Create remove-track CLI command (@cmdcolin)
  • #3341 Add BEDPE adapter type (@cmdcolin)
• core
  • #3359 Fix typos in codebase using typos-cli (@cmdcolin)

:bug: Bug Fix

• Other
  • #3377 Fix rendering and clicking synteny features when using MainThreadRpc (@cmdcolin)
  • #3375 Fix jbrowse upgrade CLI command overwriting config.json with --branch or --nightly options (@cmdcolin)
  • #3370 Fix error with SNPCoverage not rendering MM tag modifications in some cases (@cmdcolin)
  • #3366 Fix ability to use LGV synteny track on inverted alignments (@cmdcolin)
  • #3348 Fix for breakpoint split view and circular view issues with <TRA> type entries in v2.2.1 (@cmdcolin)
• core
  • #3369 Fix uncaught promise errors and add lint rule for catching these (@cmdcolin)

:memo: Documentation

• #3347 Reduce number of quickstart guides (@cmdcolin)

:house: Internal

• core
  • #3368 Create base "Dialog" component to standardize dialogs across codebase (@cmdcolin)
• text-indexing
  • #3344 fix yarn build error in Windows (@Lilas-w)

Committers: 2

• Colin Diesh (@cmdcolin)
• @Lilas-w