@jbrowse/core - npm Package Versions

1.6.8 (2022-03-25)

<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-breakpoint-split-view | | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @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-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @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
  • #2847 Add option to color all the letters on all the reads to the pileup renderer (@cmdcolin)
  • #2849 Avoid drawing intron subfeatures for gene glyphs (@cmdcolin)
  • #2835 Hide add track and connection menu items when using embedded component (@carolinebridge-oicr)
  • #2836 Display low-quality modifications in SNPCoverage renderer for MM tag (@cmdcolin)
• core
  • #2809 Optimizations for alignments tracks and BAM parsing (@cmdcolin)
  • #2828 Change calculation for number of webworkers for web/desktop (@cmdcolin)
  • #2829 Allow user to specify number of workers (@garrettjstevens)
  • #2775 New SVG gene glyph with directional arrows (@cmdcolin)

:bug: Bug Fix

• Other
  • #2852 Fix misaligned features under breakpoint split view (@cmdcolin)
  • #2844 Fix layout of small features without labels for SvgFeatureRenderer (@cmdcolin)
  • #2839 Fix the drawing of SNP height when the SNPCoverage track is using log scale (@cmdcolin)
  • #2825 Fix tracklabels positioning not updating in UI after user selection (@cmdcolin)
• core
  • #2841 Fix alignments tracks loading excessive data on chromosomes where no features exist (@cmdcolin)
  • #2829 Allow user to specify number of workers (@garrettjstevens)

Committers: 3

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

1.6.7 (2022-03-16)

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

| Package | Download | | ------------------------------------ | ----------------------------------------------------------------- | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-comparative-adapters | | | @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-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @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/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

• #2820 Add optimization for BAM and unzip operations (@cmdcolin)

:bug: Bug Fix

• #2821 Fixup scroll on wiggle tracks with trackLabels->offset (@cmdcolin)
• #2819 Fix bug in desktop where first track gets stuck loading (@garrettjstevens)

Committers: 2

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

1.6.6 (2022-03-15)

<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-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-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-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-predefined-sessions | | | @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
  • #2796 Add collapsible accordion sections in configuration editor (@cmdcolin)
  • #2791 Add new coloring options for dotplot and ability to "rectangularize" dotplot view (@cmdcolin)
  • #2741 Allow ability to enter a space-separated locstring to open a list of regions (@cmdcolin)
  • #2725 Refactor InternetAccounts, add standard getFetcher (@garrettjstevens)
  • #2787 Display the total bp viewed in the header of the dotplot view (@cmdcolin)
  • #2767 Wiggle and SNPCoverage look and feel improvements (@cmdcolin)
  • #2746 Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view (@cmdcolin)
• Other
  • #2799 Exit process after rendering to speed up jb2export (@cmdcolin)
  • #2793 Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 (@cmdcolin)
  • #2761 Add a --clean argument to jbrowse upgrade to clean up old files (@cmdcolin)
  • #2760 Make a configurable refNameColumn in RefNameAliasAdapter (@cmdcolin)

:bug: Bug Fix

• core
  • #2798 Fix bug where web worker would sometimes be called before it was ready (@garrettjstevens)
• Other
  • #2797 Fix crash plotting methylation in sparse regions (@cmdcolin)
  • #2782 Fix display of cytobands when horizontally flipped (@cmdcolin)
  • #2678 Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads (@cmdcolin)
  • #2774 Fix overwriting broken symlink with --force in add-track CLI (@cmdcolin)
  • #2773 Fix using global stats autoscale on wiggle tracks (@cmdcolin)
  • #2766 Add a check for empty content blocks to fix rare empty stats estimation (@cmdcolin)

:memo: Documentation

• #2804 Add note about additional pre-requisites to README (@cmdcolin)
• #2762 Add bookmark widget docs to user guide (@cmdcolin)

:house: Internal

• #2813 Create codeVerifierPKCE only when needed (@garrettjstevens)
• #2808 Polyfill window.crypto.getRandomValues in tests (@garrettjstevens)

Committers: 2

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

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>