Release v1.0.3

This release of JBrowse Web includes several improvements and bug fixes, including:

• Search and dropdown combined into single intuitive component on linear genome view
• Big alignment track enhancements
  • Added sort by tag to sorting options
  • Added ability to color by preset options such as "base pair", "mapping quality", and "tag"
  • Added ability to filter by preset options such as "read paired" and "read reverse strand"
• Feature detail widget now shows subfeature details
• Added --branch and --nightly flags for create and upgrade CLI commands
• Improved admin server GUI
• Additional track menu options for wiggle and SNP coverage tracks such as "autoscale", "log scale" and "histogram fill"
• Improved build system for external plugins (check out our new plugin template at https://github.com/GMOD/jbrowse-plugin-template)

1.0.3 (2021-01-11)

Packages in this release

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

🚀 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 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)

📝 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)

🏠 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