v1.6.4 Release

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. See the URL params API docs for more info
• 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.

Also check out the recording and notes from our PAG 2022 tutorial session!

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

note that 1.6.0-1.6.3 were slightly buggy and collected into 1.6.4 here

Downloads

• v1.6.4

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.

🚀 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
  • #2680 Improve error handling on jbrowse desktop open sequence dialog (@cmdcolin)
  • #2670 Add mashmap PAF support (@cmdcolin)
  • #2659 Draw size of deletion on reads in alignments track (@cmdcolin)
• __mocks__, core
  • #2165 Add ability to create new sessions solely from a "session spec" in the URL (@cmdcolin)

🐛 Bug Fix

• core
  • #2688 Fix adapterType dropdown in add track widget (@cmdcolin)
  • #2654 Fix broken @jbrowse/img by adding babel config back to core (@cmdcolin)
• Other
  • #2686 Use path.resolve to fix --load symlink in jbrowse CLI (@cmdcolin)
  • #2660 Fix custom glyphs to apply to features without subfeatures (@bbimber)
  • #2652 Fix "module" of embedded React views (@garrettjstevens)

📝 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
  • #2657 Fix hot reload using yarn resolution on react-error-overlay (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• @bbimber