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 #595
• Improve transcript widget edit location action by @shashankbrgowda in #598
• Feature expand/contract rows for feature labels in LinearApolloSixFrameDisplay by @haessar in #579
• Show details widget when we click on feature in gene glyph by @shashankbrgowda in #576
• Show feature details widget on click when in LASFD by @haessar in #602
• Add ability to merge and split exons by @dariober in #574
• Show all genes in the region as destination when adding feature from evidence track by @shashankbrgowda in #588
• Alternate transcripts filtering for LinearApolloSixFrameDisplay by @haessar in #591
• Update Cypress tests to work on latest JBrowse by @garrettjstevens in #614
• Fix and improve adding feature from BAM track to Apollo track by @shashankbrgowda in #607
• Make context menu list all possible features for that location by @dariober in #618
• Add open transcript details option on right click of child feature by @shashankbrgowda in #608
• Print gff_id when reporting errors by @dariober in #610
• New gene or transcript must have strand set by @dariober in #619
• Fix loading non-Apollo plugins from stored config by @garrettjstevens in #613
• Split docker build action by platform arch by @amorison in #616
• Add "Merge transcripts" action by @dariober in #604
• Add option in UI to download GFF without FASTA by @dariober in #625
• Add ability to configure assembly aliases in the UI by @shashankbrgowda in #620
• Fix undo only undoing the last change by @dariober in #622
• Improve click and drag actions in LASFD by @haessar in #624
• Fix:Update CDS locations for translation trim without validation by @shashankbrgowda in #609
• Fix copy to clipboard not working in some contexts by @garrettjstevens in #627
• Resize gene/transcript after deleting exon by @dariober in #632
• Fix reverse strand protein translation in sequence panel by @garrettjstevens in #628
• Update test image snapshots by @garrettjstevens in #648
• Context menu list for LASFD by @haessar in #644
• Make the "hovered feature" available to all displays on the session by @garrettjstevens in #641
• Add custom display to reference sequence track, don't render sequence on Apollo track by @garrettjstevens in #642
• Fix LASFD tooltip rendering bug by @haessar in #651
• Fix file path retrieval in desktop by @garrettjstevens in #652
• Bring LASFD into line with recent changes to reference sequence track by @haessar in #655
• Add justfile and instructions for developers by @amorison in #638
• Add more custom component extension points to the transcript widget by @garrettjstevens in #649
• Redo functionality - issue #629 by @dariober in #645
• Add menu item to hide/show check results by @haessar in #653
• Keep all attributes of merged features by @dariober in #640
• Add sequence length to and reformat the sequence panel FASTA header by @dariober in #663
• Fix wrapping of cDNA sequence by @dariober in #667
• Cluster check results to improve performance by @haessar in #664
• Add ability to change zoom display threshold by @haessar in #668
• Fix assembly not persisting in desktop when opened vi UI by @garrettjstevens in #670
• Add canonical splice site check, improve check/check result testing #636 by @dariober in #657
• Improve navigatation: go to up/downstream exon, go to from table editor by @dariober in #671
• Fix models not getting cleaned up, including multiple websocket fix by @garrettjstevens in #656
• Update display of selected feature, select a feature when adding it by @garrettjstevens in #674
• Introduce locked annotation mode (#659) by @dariober in #675
• Reorganize and add icons to top-level Apollo menu by @garrettjstevens in #676
• Add arrows on transcript line to show strand by @garrettjstevens in #677
• apollo-cli: new desktop cmd generates/opens jbrowse files by @amorison in #666
• Background color for non coding transcripts #660 by @dariober in #678
• Update JBrowse and MUI dependencies by @garrettjstevens in #679

New Contributors

• @amorison made their first contribution in #616

Full Changelog: v0.3.6...v0.3.8