Colin Diesh

note: i am not exactly sure why scrolling around in firefox starts to enable the alpha blending

The term "synteny track" is not my favorite thing, but this would be a bit tricky to change. There are sort of two things at stake a) the term synteny...

note that after " f) see what the situation looks like after implementing other synteny coloring options" it may be harder to do polylines as all the elements of a...

Alternatively: create split view with dis-contiguous displayedRegions

this was added in https://github.com/GMOD/jbrowse-components/pull/4561 the code is a little hacky IMO relying on feature.type which i feel is a bit free-text-y for vcf features but it works for now...

A CLI tool could be made to restore the lost functionality from set-default-session --tracks and --view not working, and make it instead set-default-session-spec or something like this

Note: The defaultSessionSpec takes priority over defaultSession, and defaultSession is not used when defaultSessionSpec is available. If this behavior is confusing, we could also make a "session spec" a special...

and just for background, the term spec is short for 'specification' in full...just specifies the parameters for the session

in order to avoid confusion between defaultSession and defaultSessionSpec, I propose now making it so it is a special type of defaultSession where defaultSession.type==='spec'

this is a good question. one thing i'm debating in this PR is that currently both the "simplified" and "full" snapshot use the "defaultSession" variable name. possibly the simplified one...