@jbrowse/plugin-alignments - npm Package Versions

1.6.0 (2022-01-28)

<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-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-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-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-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/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
  • #2679 Optimizations and usability improvements to synteny view (@cmdcolin)
  • #2677 Save user settings from LGV (@cmdcolin)
  • #2571 Add stats estimation to JB2 (@cmdcolin)
  • #2666 Add option to display curved lines and to square the dotplot and synteny views (@cmdcolin)
  • #2672 Optimize dot plot rendering (@cmdcolin)
• Other
  • #2680 Improve error handling on jbrowse desktop open sequence dialog (@cmdcolin)
  • #2670 Add mashmap PAF support (@cmdcolin)
  • #2659 Draw size of deletion on reads in alignments track (@cmdcolin)
• __mocks__, core
  • #2165 Add ability to create new sessions solely from a "session spec" in the URL (@cmdcolin)

:bug: Bug Fix

• core
  • #2688 Fix adapterType dropdown in add track widget (@cmdcolin)
  • #2654 Fix broken @jbrowse/img by adding babel config back to core (@cmdcolin)
• Other
  • #2686 Use path.resolve to fix --load symlink in jbrowse CLI (@cmdcolin)
  • #2660 Fix custom glyphs to apply to features without subfeatures (@bbimber)
  • #2652 Fix "module" of embedded React views (@garrettjstevens)

:memo: Documentation

• #2663 Add documentation for URL params and session spec (@cmdcolin)
• #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)

:house: Internal

• core
  • #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
  • #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
• Other
  • #2657 Fix hot reload using yarn resolution on react-error-overlay (@cmdcolin)

Committers: 3

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

1.5.9 (2022-01-13)

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

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @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>

:bug: Bug Fix

• #2645 Fix core by not using absolute runtime in babel (@garrettjstevens)

Committers: 1

• Garrett Stevens (@garrettjstevens)

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

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @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>

1.5.7 (2022-01-13)

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

| Package | Download | | ---------------------------- | -------- | | @jbrowse/plugin-dotplot-view | | | @jbrowse/desktop | | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• #2632 Add vertical resize handle to dotplot view (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

1.5.6 (2022-01-12)

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

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @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
  • #2629 Add ability to get parent feature in jexl syntax with either parent(feature) or get(feature,'parent') (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Teresa Martinez (@teresam856)

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

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @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>

1.5.4 (2022-01-07)

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

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @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-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-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-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-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
  • #2601 Allow opening multiple sequences from the desktop start screen (@cmdcolin)
• core
  • #2623 Adjust label width on base feature detail to enforce better alignment (@carolinebridge-oicr)

:bug: Bug Fix

• Other
  • #2612 Fix ability to remove plugins (@cmdcolin)
  • #2622 Fix GUI color editor rgba string format (@garrettjstevens)
  • #2607 Fix wiggle tooltip crash on non-numerical inputs (@cmdcolin)
• core
  • #2626 Fix bad layout resulting in features being unable to be clicked in embedded mode (@cmdcolin)

:house: Internal

• core
  • #2595 Use some newly available TypeScript types (@garrettjstevens)
  • #2576 Use TypeScript parameter properties (@garrettjstevens)

Committers: 3

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

1.5.3 (2021-12-21)

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

| Package | Download | | -------------------------- | -------------------------------------------------------- | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |

</p> </details>

:bug: Bug Fix

• development-tools
  • #2600 Fix broken published build of jbrowse/development-tools (@garrettjstevens)

Committers: 1

• Garrett Stevens (@garrettjstevens)

1.5.2 (2021-12-20)

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

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools | | @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-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-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-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
  • #2579 Add help text and help dialog for the RefNameAutocomplete (@cmdcolin)
  • #2553 Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display (@cmdcolin)
  • #2552 Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill (@cmdcolin)
  • #2509 Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer (@hextraza)
  • #2485 Only use one button, "Go", in text search ambiguous results dialog (@cmdcolin)
  • #2501 Add a tooltip to desktop session path so you can see the full path if it's cut off (@garrettjstevens)
• core
  • #2580 Make core snackbar notifications module with auto-dismissing info/success level notifications (@cmdcolin)
  • #2534 New display type for drawing arcs (@carolinebridge-oicr)
  • #2590 Add more exports that can be used by plugins (@garrettjstevens)
  • #2578 Add layouts code to core re-exports (@garrettjstevens)
  • #2523 Performance optimizations for alignments tracks, particularly those with many short reads (@cmdcolin)
  • #2500 Add RenderProps to core/pluggableElementTypes export (@garrettjstevens)
• core, development-tools
  • #2487 Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop (@garrettjstevens)

:bug: Bug Fix

• Other
  • #2594 Fix infinite loop bug while searching certain strings and handle multi-word searches better (@cmdcolin)
  • #2589 Fix occasional failures observed from running text-index command (@cmdcolin)
  • #2583 Fix for alignments track base modifications display regarding skipped bases on Mm tag (@cmdcolin)
  • #2556 Fix ability to access BigWig tracks on http basic auth for some cases (@cmdcolin)
  • #2577 Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI (@cmdcolin)
  • #2521 Fix ability to search for tracks with parentheses in tracklist (@cmdcolin)
  • #2512 Fix [object Window] issue in alignment read vs reference dialog (@cmdcolin)
  • #2499 Add missing dependency to CLI (@garrettjstevens)
• core
  • #2585 Fix ability to use "Color by methylation" on files that require refname renaming (@cmdcolin)
  • #2517 Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state (@cmdcolin)
  • #2564 Start looking for parents with parent, not self in findParentThat (@garrettjstevens)
  • #2563 Restore ability to load plugins from relative URL (@garrettjstevens)
  • #2533 Fix drawer widget minimized button being unclickable when overlapping with a view (@cmdcolin)

:memo: Documentation

• #2522 Add circular genome view storybook (@cmdcolin)
• #2508 Update docs for embedded components (@teresam856)
• #2495 Improve organization on docs landing page (@cmdcolin)

:house: Internal

• core
  • #2597 Fix flaky tests related to auth and canvas image snapshots (@cmdcolin)
  • #2504 Spreadsheet change jbrequire to es6 imports (@cmdcolin)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)
• Sebastian Benjamin (@hextraza)
• Teresa Martinez (@teresam856)