v1.0.3 Release
· 4 min read
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)
Figure showing the new feature for "color by tag" and
"sort by tag" applied to a CRAM file
Downloads
To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.
1.0.3 (2021-01-11)
🚀 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 createandjbrowse upgradecommands (@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
📝 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