Releases: GMOD/jbrowse-components
Release v1.6.9
This is a re-release of 1.6.8 to fix the Mac build of JBrowse Desktop
Release v1.6.8
We are pleased to announce the v1.6.8 release!
This release includes a change to the default gene style to use boxes instead of "chevron" features, with a directional arrowhead
Before
After
Some additional highlights
- Draws the correct the proportion of SNPs when displaying the SNPCoverage
height in log scale (thanks @gringer for reporting) - Adds more optimizations for some alignments tracks
- Adds a per-base drawing mode to alignments tracks
🚀 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
🐛 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)
Release v1.6.7
This release fixes an issue with JBrowse Desktop on v1.6.6 where the first tracks to be opened would not load.
It also adds a speed optimization for BAM files (in some cases, 5x speed improvement seen in deep coverage files), and fixes a scroll issue on wiggle tracks!
1.6.7 (2022-03-16)
Packages in this release
| 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 |
🚀 Enhancement
🐛 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)
Release v1.6.6
We are pleased to release v1.6.6!
This contains several updated synteny features, including:
- load .chain files from UCSC
- load .delta files from mummer
- load .anchors and .anchors.simple files from MCScan from the GUI
- ability to "rectangularize" the dotplot view and improved dotplot view overviews (shows total bp of selected regions)
Screenshot showing updated import form with ability to load MCScan data
Screenshot showing multiple tracks open at once, with the .anchors (green, gene
pairs) and .anchors.simple (black, larger synteny blocks) files from MCScan
shown in the dotplot view
Note: MCScan functionality existed internally but was not easy to use. The
configuration schema for MCScan anchors files changed also to load the .bed
files at startup. See the config guide for details
We also have an updated configuration editor GUI with collapsible sections
Screenshot showing new collapsible (turquoise) sections in the config editor
A number of alignments track look and feel improvements were also added. The
scale bar was made to just list the min and max values when the height is
small, clip indicator position when horizontally flipped was fixed, and the
headroom was removed making the snpcoverage take up the full height of the
small area it uses.
There have also been some changes to how internet accounts work. If you use one
of the built-in accounts like Google Drive or Dropbox, there's no need to change
anything. If you've implemented your own internet account, though, see
#2725 for more details.
🚀 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 upgradeto clean up old files (@cmdcolin) - #2760 Make a configurable refNameColumn in RefNameAliasAdapter (@cmdcolin)
🐛 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)
📝 Documentation
- #2804 Add note about additional pre-requisites to README (@cmdcolin)
- #2762 Add bookmark widget docs to user guide (@cmdcolin)
🏠 Internal
- #2813 Create codeVerifierPKCE only when needed (@garrettjstevens)
- #2808 Polyfill window.crypto.getRandomValues in tests (@garrettjstevens)
Committers: 2
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Release v1.6.5
We are pleased to announce v1.6.5!
This release features various bugfixes to the @jbrowse/cli tool, including better
support for large config files with the admin-server, and renaming --out to
--root for the admin-server.
It also includes two important fixes related to stats estimation since 1.6.4, one
where tracks would display an error on sparse tracks and another where tracks
would fail to perform stats estimation on BAM files due to a type confusion.
🚀 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 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)
📝 Documentation
- #2716 Update to node12 requirement for @jbrowse/cli (@cmdcolin)
- #2605 Developer guide reorganization and create new API document (@cmdcolin)
🏠 Internal
core- #2664 Use babel config from core in root (@garrettjstevens)
Committers: 3
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Sebastian Benjamin (@hextraza)
Release v1.6.4
This release has a couple long awaited features!
- Ability to load a session from a URL in JBrowse Web, for example,
https://jbrowse.org/code/jb2/v1.6.4/?config=test_data/volvox/config.json&loc=ctgA:2000-40000&assembly=volvox&tracks=gff3tabix_genes,volvox_filtered_vcf,volvox_microarray,volvox_cram
(note: the embedded components do not make any assumptions about the URL, so
do not have this functionality. Just the JBrowse Web package) - Stats estimation, tracks will try to estimate how much data they have to load
and hide themselves if it is determined to be too much
There are also some improvements to synteny and dotplot views. The synteny view
can now render curvy lines and "square" the views (so they each have the same
zoom level), and have individual search panels in the synteny view. You can now
also vertically resize the linear synteny view panel allowing for a taller or
shorter view! The rendering has also been sped up in both linear synteny and
dotplot views with certain code paths being up to 40x faster
Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.4/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj
🚀 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
__mocks__,core
🐛 Bug Fix
core- Other
📝 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)
🏠 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
Committers: 3
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- @bbimber
Release v1.5.9
Fixes a babel issue that affected users of embedded components. v1.5.5-1.5.8 were affected by babel misconfigurations but this is now fixed.
🐛 Bug Fix
- #2645 Fix core by not using absolute runtime in babel (@garrettjstevens)
Committers: 1
- Garrett Stevens (@garrettjstevens)
Release v1.5.8
This release fixes an important issue where @jbrowse/react-linear-genome-view and other embedded packages did not work with v1.5.5 due to a babel misconfiguration apologies to all affected! This release fixes this issue, and adds a vertically drag handle to the dotplot view, and allows users to get the parent feature in jexl expressions.
Also note that v1.5.6 and v1.5.7 were not published to npm properly due to broken uploads but are fixed here
🚀 Enhancement
Release v1.5.5
This release fixes an important bug for users of @jbrowse/react-linaer-genome-view where some features would not be able to be clicked in v1.5.3 and v1.5.2.
It also adds some better layout in the feature details panel, improved typescript interfaces, and allows users to open multiple genome assemblies from the start screen in JBrowse Desktop
The v1.5.4 was skipped due to a publishing error
Enjoy
Release v1.5.3
This release fixes @jbrowse/development-tools, which was broken in v1.5.2, and is otherwise identical to v1.5.2. See the v1.5.2 release announcement for details about that release.
1.5.3 (2021-12-21)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |
🐛 Bug Fix
development-tools- #2600 Fix broken published build of jbrowse/development-tools (@garrettjstevens)
Committers: 1
- Garrett Stevens (@garrettjstevens)