Release v2.3.1

[cmdcolin]

Hello all! This release adds some great new features!

• New "arc" and "read cloud" alignments track modes which render long range
  connections between read pairs/split reads. These views have a big impact on
  being able to visualize structural variants.

• We now automatically optimize the "prefix size" for our trix indexes created
  by jbrowse text-index which should help solve issues with slow text
  searching.

• We now refer to many pluggable elements by a "display name" instead of the
  coded class name so we have instead of "LinearGCContentDisplay" -> "GC content
  display".

New alignments track displays

We created a new display mode that changes the "pileup" of reads into "arcs"
which connects both paired-end reads and split-long read alignments.

New track menu showing the ability to replace the "lower panel" with arc display
or read cloud display

The arc view and read cloud view rendering across discontinuous displayedRegions

A zoomed in view of long-reads (top) and paired-end reads (bottom) at the
breakpoint of a large deletion

Easily toggleable "compact" view of alignments

We now have an easily toggleable compact setting on alignments tracks
(previously had to manually change feature height)

Optimized prefix size for text search indexing

Previously, if indexing long gene IDs with jbrowse text-index it would often
be slow because the "trix" format is generally optimized for short gene symbols.
We added the --prefixSize parameter in previous jbrowse versions to allow
optimizing for specific gene ID lengths, but this was sort of a magic number. Now,
jbrowse text-index will automatically calculate the --prefixSize if none is
provided, which tries to get an even ~64kb bin size. Let us know how it goes for
your data!

Re-install the CLI tools with e.g. npm install -g @jbrowse/cli to get the
latest version with this feature.

Moved "Track Hub Registry" plugin to plugin store

We removed the "Track Hub Registry" plugin, which was previously a "core
plugin", to the plugin store. This will allow us to update the plugin over time
and respond better to issues when they change their remote API.

---

This discussion was created from the release Release v2.3.1.