@jbrowse/development-tools - npm Package Versions

1.3.0 (2021-05-24)

<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-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-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @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-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/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #2001 Make tracks added using the add track widget a session track if not in adminMode (@cmdcolin)
  • #1980 Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist (@cmdcolin)
  • #1977 Upgrade @material-ui/data-grid (@cmdcolin)
• core
  • #1982 Allow manually specifying adapter type if filename does not match expected pattern (@cmdcolin)
  • #1975 Allow local files on the users computer to be opened as tracks in jbrowse-web (@cmdcolin)
  • #1865 Show modified bases using MM and MP/ML tags in BAM/CRAM (@cmdcolin)
  • #1984 Better feature details when there are short arrays of json supplied as feature data (@cmdcolin)
  • #1931 Create in app graphical plugin store (@elliothershberg)

:bug: Bug Fix

• core
  • #1985 Avoid error calculating UTR on features that have no exon subfeatures (@cmdcolin)
  • #1954 Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering (@cmdcolin)
  • #1963 Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components (@cmdcolin)
  • #1945 Fix hic not being able to render due to incorrect lazy loading (@cmdcolin)
• Other
  • #1956 Fix connection behavior (@garrettjstevens)
  • #1966 Fix ability to use add-track force on symlink tracks (@cmdcolin)
  • #1951 Fix breakpoint split view demo configuration on website (@cmdcolin)

:memo: Documentation

• #2002 Add @jbrowse/img to homepage (@cmdcolin)
• #2007 Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details (@cmdcolin)
• #1976 reorganize the demo page to emphasize the cancer sv demo more (@rbuels)
• #1952 Add demo for 1000 genomes extended trio dataset to website (@cmdcolin)
• #1862 Add example for using a build-time included plugin to storybook (@cmdcolin)

:house: Internal

• Other
  • #2003 Make SNPCoverage independently generate the modifications tag-color mapping (@cmdcolin)
• core, development-tools
  • #1930 Upgrade react scripts+react to latest versions (@cmdcolin)

Committers: 4

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)

1.0.3 (2021-01-11)

<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-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-hic | | | @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-spreadsheet-view | | | @jbrowse/plugin-trackhub-registry | | | @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/protein-widget | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #1560 Provide a dialog to add extra genomic context for linear read vs. ref visualization (@elliothershberg)
  • #1604 Add ability to filter for read name to the alignments filter dialog (@cmdcolin)
  • #1599 Replace 'show all regions' with 'show all regions in assembly' (@cmdcolin)
  • #1595 Admin server GUI enhancements (@elliothershberg)
  • #1584 Restructure demo page and release cancer demo (@elliothershberg)
  • #1579 Create --branch and --nightly flags for jbrowse create and jbrowse upgrade commands (@cmdcolin)
  • #1575 Improve mobx-state-tree type validation errors (@cmdcolin)
  • #1574 Make softclip indicator black if no seq available (@cmdcolin)
  • #1554 Coloring options with simple color for tag (@peterkxie)
  • #1565 Rename jbrowse cli add-track --type to --trackType (@cmdcolin)
  • #1558 Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo (@cmdcolin)
  • #1533 Display file headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix package versions (@cmdcolin)
  • #1541 Add more info about adding a PAF file to the synteny import form (@cmdcolin)
  • #1509 Combine Search and Dropdown component on LGV (@teresam856)
  • #1530 Add spreadsheet filter support for derived columns (@elliothershberg)
  • #1483 Add session export to and import from file (@garrettjstevens)
  • #1519 Add autoSql to the bigBed "About this track" dialog (@cmdcolin)
• core
  • #1531 Add track menu options for autoscale, log scale, histogram fill, setting min/max score, and zoom level/resolution for wiggle/snpcoverage tracks (@cmdcolin)
  • #1473 Color, filter, and sort options for the alignments (@cmdcolin)
  • #1576 Add location string to tooltip for wiggle and SNPCoverage tracks (@cmdcolin)
  • #1529 Display subfeatures in feature details widget (@cmdcolin)
• core, development-tools
  • #1578 Update build system for external plugins (@garrettjstevens)

:bug: Bug Fix

• Other
  • #1608 Take into account offsetX of the rubberband on scalebar zooming (@cmdcolin)
  • #1597 Fix crash when there are undefined references in the state tree e.g. when a track is deleted but still referred to by a session (@peterkxie)
  • #1598 Disable 'copy to clipboard' while share url being generated (@peterkxie)
  • #1589 Fix the display of trackhub registry results (@cmdcolin)
  • #1573 Update hic-straw to fix error for hic files with many scaffolds (@cmdcolin)
  • #1563 Remove softclip and hardclip from being counted as SNPs in the SNPCoverage (@cmdcolin)
  • #1559 Avoid errors from breakpoint split view related to getBoundingClientRect on null track (@cmdcolin)
  • #1540 Fix memory leak when side scrolling LGV blocks (@cmdcolin)
  • #1534 Fix breakpoint split view showing too many connections for paired end ends (@cmdcolin)
  • #1524 Move loading flag for spreadsheet import wizard to volatile to avoid it persisting across refresh (@cmdcolin)
  • #1521 Add missing dep to react-linear-genome-view (@garrettjstevens)
• core
  • #1587 Fix positioning of scalebar tooltips, overview scalebar plotting, and refName label positioning when displaying many regions (@cmdcolin)
  • #1547 Fix analytics crashing when using plugins (@cmdcolin)

:memo: Documentation

• #1594 Add GFF3 example to quickstart (@cmdcolin)
• #1581 Add some features that are missing from jbrowse 2 to the feature comparison table (@cmdcolin)
• #1558 Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo (@cmdcolin)
• #1537 Add CONTRIBUTING.md with tips for getting started with codebase (@cmdcolin)

:house: Internal

• #1606 Upgrade @testing-library/react and improve test reliability (@cmdcolin)
• #1555 Remove the TextDecoder/TextEncoder polyfill (@cmdcolin)
• #1522 Update oclif and remove now unnecessary file copy (@garrettjstevens)

Committers: 6

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)
• Teresa Martinez (@teresam856)
• @Akusem

v1.0.2 (2020-12-02)

<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-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-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @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-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/protein-widget | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• core
  • #1513 Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX (@elliothershberg)

:bug: Bug Fix

• Other
  • #1514 react-linear-genome-view bug fixes (@garrettjstevens)
  • #1517 Fix the use of filtering display on desktop (@cmdcolin)
  • #1512 Fix setting maxDisplayedBpPerPx for pileup display, helps prevent too large an area from being rendered (@cmdcolin)
  • #1442 Change track selector togglebutton to normal button (@cmdcolin)
  • #1506 Fix horizontally flipped translation frames position (@cmdcolin)
  • #1501 Fix CLI to allow jbrowse create to download newer monorepo tag format (@cmdcolin)
• core
  • #1505 Fix loading of local files in jbrowse-desktop (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)

v1.0.1 (2020-11-25)

<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-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @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-filtering | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-hic | | | @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-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/protein-widget | | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>

:rocket: Enhancement

• Other
  • #1462 Allow importing gzip and bgzip files in the spreadsheet and SV inspector (@cmdcolin)
  • #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
  • #1455 Add the ability to use connection across refreshes in jbrowse-web using session connections (@peterkxie)
  • #1439 1381 improve assembly add form (@elliothershberg)
  • #1433 Make add track warning a bit more lenient (@garrettjstevens)
  • #1420 Add the assembly manager feature to jbrowse-desktop (@elliothershberg)
• core
  • #1458 Add three frame translation to the sequence track (@cmdcolin)
  • #1453 Change "Factory reset" to "Reset session" in jbrowse-web (@teresam856)
  • #1441 New icon for the track selector (@cmdcolin)
  • #1438 Improve assembly loading time by moving to main thread (@cmdcolin)
  • #1434 Create separate config schema for ReferenceSequenceTrack (@elliothershberg)

:bug: Bug Fix

• core
  • #1491 Fix ability to add a PAF synteny track with add-track (@cmdcolin)
  • #1470 Avoid rendering the literal string 'null' in the feature details (@cmdcolin)
• Other
  • #1489 Fix long read vs ref CIGAR rendering for horizontally flipped synteny view (@cmdcolin)
  • #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
  • #1472 Wait on assemblies that are being tracked by the assemblyManager only (@cmdcolin)
  • #1466 Avoid rendering the display and renderer settings in the about this track dialog (@cmdcolin)
  • #1461 Fix usage of jbrowse-cli on node 10.9 related to fs.promises (@cmdcolin)
  • #1452 Bug: search box disappears from LGV header on smaller widths (@teresam856)
  • #1432 Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web (@teresam856)
  • #1431 Fix connection tracks not showing up in track selector (@garrettjstevens)
  • #1428 Fix the listVersions behavior of the jbrowse-cli returning duplicate entries (@cmdcolin)
  • #1422 Fix crash from empty ALT field in VCF (@cmdcolin)
  • #1413 Fix ability to add CRAM tracks using the web based add-track GUI (@cmdcolin)

:memo: Documentation

• #1435 Updates to quickstart guides (@garrettjstevens)

:house: Internal

• Other
  • #1437 Use lerna-changelog for changelog generation (@cmdcolin)
  • #1465 Establish minimum node version of 10.4 for using jbrowse-cli tools (@cmdcolin)
  • #1454 Fix GH workflow build (@elliothershberg)
  • #1448 Move building and testing from Travis to GitHub Workflow (@garrettjstevens)
  • #1450 Fix website build (@garrettjstevens)
• core
  • #1468 Have assembly manager get plugin manager from factory function args (@garrettjstevens)

Committers: 5

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Teresa Martinez (@teresam856)
• @peterkxie