Release v2.17.0

This release adds:

• Improved and bugfixed rendering of modified bases from BAM/CRAM files, particularly, it matches in many ways the IGV rendering of modified bases [^1]
• Improved performance for ultra-long reads from Nanopore, especially with zooming in and out and scrolling because it caches the mismatches instead of re-calculating them repeatedly [^2]
• Improved performance for wiggle tracks, multi-wiggle tracks, and SNP coverage tracks, particularly changing the height for these track types produces less re-rendering
• A new data adapter loading BLAST tabular -outfmt 6 alignments for the synteny view
• Fixed interpretation of the 'ts' tag from minimap2 for RNA-seq strandedness
• Improved bedMethyl support

figure showing updated modifications rendering, and bedMethyl as a "MultiQuantitativeTrack"

example of the BLAST tabular adapter, showing TBLASTX results

[^1] Importantly, JBrowse 2 now takes into account the ML tag (likelihood) to better report the results when tools are providing low probability modification likelihoods, especially for when there are multiple modification possibilities at each position (e.g. commonly outputted from Dorado which reported as 'm' and 'h' probabilities, we now only choose the highest likelihood for reporting, which is in line with interpretation from the MM/ML tag specification)

[^2] As part of this change, the internals of BAM/CRAM records have been changed. If you have code that was directly accessing any internal attributes of these records, it may not work anymore. Please use the feature.get('...') on features to get data of interest. The .get(...) method is the only "official" API for accessing data on feature objects, and contact us if you run into any problems!

2.17.0 (2024-11-18)

🚀 Enhancement

• core
  • #4662 Add better handling for bedMethyl files (@cmdcolin)
  • #4652 Reduce re-rendering on quantitative and snpcoverage track height adjustments (@cmdcolin)
  • #4651 Add mismatches cache to improve performance on ultra-long reads (@cmdcolin)
• Other
  • #4649 Add support for displaying SNPs in "no_ref" CRAM files (@cmdcolin)
  • #4627 Create BLAST tabular adapter (@garrettjstevens)

🐛 Bug Fix

• Other
  • #4647 Improved rendering of modifications (@cmdcolin)
  • #4646 Fix mouseover pixelation on linear synteny view (@cmdcolin)
• core
  • #4639 Fix RNA-seq stranded arc coloring, change the color of RNA-seq introns, and improve compact rendering (@cmdcolin)
  • #4638 Fix rendering of UCSC repeatmasker BigBed and BED files (@cmdcolin)

🏠 Internal

• core
  • #4648 Run codemod fix for some MUI deprecated props (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.81s.