Beta Version 0.3.8
We are excited to release version v0.3.8
of Apollo 3, which includes many new
features inspired by feedback from users. Below are some of the changes since
v0.3.6
that we'd like to highlight.
Also, when updating Apollo 3 to this version, please make sure to also update
JBrowse 2 to at least v3.6.5
as there are some important stability
improvements that require JBrowse 2 to be updated to take effect.
New features
Apollo Reference Sequence Track
Prior to this release, Apollo would draw the sequence directly on the "Annotations" track if you were zoomed in close enough. However, this could cause the annotations to jump around depending on the zoom level, and there was no way to hide the sequence for users who didn't want to see it.
In this release, instead of being drawn directly in the "Annotations" track, the sequence is available as the default display in the built-in "Reference sequence" track, allowing it to have its own dedicated space. The interactions with the "Annotations" track, such as highlighting the currently hovered CDS, still work the same, and if needed the default JBrowse sequence display can be toggled on from the track menu.
Merge and split exons
There is a new command that will merge two exons into a single one, as well as an accompanying command to split an exon into two separate exons.
Merge transcripts
Transcripts can now be merged, and Apollo 3 will create a new transcript with its subfeatures automatically calculated from the overlap of the source transcripts.
Redo
In addition to the existing "Undo" functionality, "Redo" is also now available from the top-level Apollo menu.
Go to neighboring exons
A new method of navigation is available in the form of the menu items "Go to upstream/downstream exon". This is especially useful when navigating at a high zoom level in genes with large introns.
Locked mode
A new option is available from the top-level Apollo menu that allows you to lock and unlock editing. When locked, no edits are able to be made, allowing you to be able to freely explore the data without risk of accidental editing.
Improved functionality
Labels in six-frame view
The six-frame view now provides labels for its features. These can also be disabled in the track menu for a more compact view.
Filter transcripts in six-frame view
In the six-frame view, if there are alternate transcripts and you want to focus on just one of them, you can now select which transcripts to filter out of the current view.
Copy feature from alignments track into an existing gene
Read features in a JBrowse alignments track (such as from a BAM or CRAM file) can now be copied as transcript features into an existing gene, in addition to the being able to create a new gene.
Right-click menu lists all features for a location
The right-click (a.k.a. context) menu for gene glyphs has been updated to show actions for any features that overlap the current location.
Check results clustering
Check result warning symbols are now clustered together when they overlap, which helps prevent clutter in the display. The warning symbols can also be turned off completely from the track menu.
Background colors for noncoding transcripts
Features with the type "pseudogene" or transcripts with the type "pseudogenic_transcript" are now rendered with a blue background so they can be easily visually identified. Similarly, any other transcripts that do not have a CDS (such as those of type "lncRNA") are rendered with a red background.
Selection of added features
When you add a new feature, whether top-level or a child feature (i.e. a transcript), the feature is now selected in the UI allowing you to more easily identify it.
For more information
For more details on any of the changes mentioned as well as many more changes that have been made, please reference the associated GitHub issues.
- Improve click and drag actions by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/595
- Improve transcript widget edit location action by @shashankbrgowda in https://github.com/GMOD/Apollo3/pull/598
- Feature expand/contract rows for feature labels in LinearApolloSixFrameDisplay by @haessar in https://github.com/GMOD/Apollo3/pull/579
- Show details widget when we click on feature in gene glyph by @shashankbrgowda in https://github.com/GMOD/Apollo3/pull/576
- Show feature details widget on click when in LASFD by @haessar in https://github.com/GMOD/Apollo3/pull/602
- Add ability to merge and split exons by @dariober in https://github.com/GMOD/Apollo3/pull/574
- Show all genes in the region as destination when adding feature from evidence track by @shashankbrgowda in https://github.com/GMOD/Apollo3/pull/588
- Alternate transcripts filtering for LinearApolloSixFrameDisplay by @haessar in https://github.com/GMOD/Apollo3/pull/591
- Update Cypress tests to work on latest JBrowse by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/614
- Fix and improve adding feature from BAM track to Apollo track by @shashankbrgowda in https://github.com/GMOD/Apollo3/pull/607
- Make context menu list all possible features for that location by @dariober in https://github.com/GMOD/Apollo3/pull/618
- Add open transcript details option on right click of child feature by @shashankbrgowda in https://github.com/GMOD/Apollo3/pull/608
- Print gff_id when reporting errors by @dariober in https://github.com/GMOD/Apollo3/pull/610
- New gene or transcript must have strand set by @dariober in https://github.com/GMOD/Apollo3/pull/619
- Fix loading non-Apollo plugins from stored config by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/613
- Split docker build action by platform arch by @amorison in https://github.com/GMOD/Apollo3/pull/616
- Add "Merge transcripts" action by @dariober in https://github.com/GMOD/Apollo3/pull/604
- Add option in UI to download GFF without FASTA by @dariober in https://github.com/GMOD/Apollo3/pull/625
- Add ability to configure assembly aliases in the UI by @shashankbrgowda in https://github.com/GMOD/Apollo3/pull/620
- Fix undo only undoing the last change by @dariober in https://github.com/GMOD/Apollo3/pull/622
- Improve click and drag actions in LASFD by @haessar in https://github.com/GMOD/Apollo3/pull/624
- Fix:Update CDS locations for translation trim without validation by @shashankbrgowda in https://github.com/GMOD/Apollo3/pull/609
- Fix copy to clipboard not working in some contexts by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/627
- Resize gene/transcript after deleting exon by @dariober in https://github.com/GMOD/Apollo3/pull/632
- Fix reverse strand protein translation in sequence panel by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/628
- Update test image snapshots by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/648
- Context menu list for LASFD by @haessar in https://github.com/GMOD/Apollo3/pull/644
- Make the "hovered feature" available to all displays on the session by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/641
- Add custom display to reference sequence track, don't render sequence on Apollo track by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/642
- Fix LASFD tooltip rendering bug by @haessar in https://github.com/GMOD/Apollo3/pull/651
- Fix file path retrieval in desktop by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/652
- Bring LASFD into line with recent changes to reference sequence track by @haessar in https://github.com/GMOD/Apollo3/pull/655
- Add
justfile
and instructions for developers by @amorison in https://github.com/GMOD/Apollo3/pull/638 - Add more custom component extension points to the transcript widget by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/649
- Redo functionality - issue #629 by @dariober in https://github.com/GMOD/Apollo3/pull/645
- Add menu item to hide/show check results by @haessar in https://github.com/GMOD/Apollo3/pull/653
- Keep all attributes of merged features by @dariober in https://github.com/GMOD/Apollo3/pull/640
- Add sequence length to and reformat the sequence panel FASTA header by @dariober in https://github.com/GMOD/Apollo3/pull/663
- Fix wrapping of cDNA sequence by @dariober in https://github.com/GMOD/Apollo3/pull/667
- Cluster check results to improve performance by @haessar in https://github.com/GMOD/Apollo3/pull/664
- Add ability to change zoom display threshold by @haessar in https://github.com/GMOD/Apollo3/pull/668
- Fix assembly not persisting in desktop when opened vi UI by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/670
- Add canonical splice site check, improve check/check result testing #636 by @dariober in https://github.com/GMOD/Apollo3/pull/657
- Improve navigatation: go to up/downstream exon, go to from table editor by @dariober in https://github.com/GMOD/Apollo3/pull/671
- Fix models not getting cleaned up, including multiple websocket fix by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/656
- Update display of selected feature, select a feature when adding it by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/674
- Introduce locked annotation mode (#659) by @dariober in https://github.com/GMOD/Apollo3/pull/675
- Reorganize and add icons to top-level Apollo menu by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/676
- Add arrows on transcript line to show strand by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/677
- apollo-cli: new
desktop
cmd generates/opens jbrowse files by @amorison in https://github.com/GMOD/Apollo3/pull/666 - Background color for non coding transcripts #660 by @dariober in https://github.com/GMOD/Apollo3/pull/678
- Update JBrowse and MUI dependencies by @garrettjstevens in https://github.com/GMOD/Apollo3/pull/679
New Contributors
- @amorison made their first contribution in https://github.com/GMOD/Apollo3/pull/616
Full Changelog: https://github.com/GMOD/Apollo3/compare/v0.3.6...v0.3.8