@jbrowse/plugin-alignments - npm Package Versions

1.6.5 (2022-02-18)

<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-dotplot-view | | | @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-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

• #2736 Add better display of error state in dotplot view and load gzipped PAF files (@cmdcolin)
• #2705 Increase admin-server payload limit (@garrettjstevens)

:bug: Bug Fix

• Other
  • #2758 Use VariantTrack for plaintext VCF type (@cmdcolin)
  • #2738 Add better catch for XS and TS tag detection from CRAM (@cmdcolin)
  • #2733 Use sparse array for alignments coverage to fix bug viewing large sparse regions (@cmdcolin)
  • #2734 Use node fetch instead of follow-redirects in cli (@cmdcolin)
  • #2726 Handle .bgz file extension for text-index (@cmdcolin)
  • #2727 Add engines 16 to @jbrowse/img (@cmdcolin)
  • #2723 Make jbrowse desktop more robust to errors when reading recent sessions file (@cmdcolin)
  • #2715 Change --target to --root for jbrowse CLI admin-server (@cmdcolin)
• core
  • #2757 Fix type confusion with stats estimation causing BAM files to fail byte size calculation (@cmdcolin)
  • #2750 Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox (@cmdcolin)
  • #2719 Avoid uninitialized state during stats estimation (@cmdcolin)
  • #2707 Fix ability to use authenticated assembly files (@garrettjstevens)
  • #2695 Fix disabled state on the linear genome view track labels dropdown menu (@cmdcolin)

:memo: Documentation

• #2716 Update to node12 requirement for @jbrowse/cli (@cmdcolin)
• #2605 Developer guide reorganization and create new API document (@cmdcolin)

:house: Internal

• core
  • #2664 Use babel config from core in root (@garrettjstevens)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Sebastian Benjamin (@hextraza)

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

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

</p> </details> <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> <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>

1.6.0 (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>