Provide a dialog to add extra genomic context for linear read vs. ref visualization

[elliothershberg]

This PR proposes to expand the start and end of the reference linear view when opening a linear vs. ref view. I think that this helps avoid cutting off details on the reference genome surrounding the read.

Example:

The current solution is add a region that is the length of the read to the left and right side of the read for the reference.

i.e.

This was motivated by #1322

[cmdcolin]

On some level, I like the precision of the current solution, because it matches everything up perfectly. I might prefer if it were an option to add extra space

[cmdcolin]

To me, the breakpoint split view itself could use something helpful that provides genomic context of more side by side of a breakpoint, but the read vs ref is based on a continuous alignment of the read versus the reference?

[cmdcolin]

This is something I have tried to propose a bunch of times with #655 and is probably not that technically difficult to set up, but would be pretty valuable

[elliothershberg]

@cmdcolin all good points. Do you have any thoughts for a straightforward way to implement this type of zooming out being optional? One way could be to create the reference view with the proposed new start and end, but (if possible) start zoomed in to the previous view. I think it would really help this view to not be cut off to seeing some surrounding parts of the region.

Re #655 , sounds cool. Would be neat to be able to toggle back and forth between side by side and stacked.

[rbuels]

I'm a little confused ... could somebody paste before and after screenshots of what this change looks like?

[cmdcolin]

Here is an example from our docs

Before

After

This is an interesting one because, while I don't like how it visually looks afterwards, it is a good example because after Elliot's change, it shows that the read is aligning to basically regions of copies of the same gene (WASH* in all three panels), which was not as obvious in the panel without the context.

[cmdcolin]

Maybe using the word "don't like how it looks afterwards is too strong" but it is "less continuous of an alignment"

[cmdcolin]

By creating this example, it does suggest that adding this change could be useful. Possibly with a popup box that let's you configure the window size?

[elliothershberg]

Nice, thanks @cmdcolin for adding the screenshots. It's funny, I personally like the way it looks visually a bit more!

So what is your thought on workflow:

click linear vs. ref --> popup for determining window size --> view opens?

I do like the way it automatically opens right now, but could do a branch w/ this to see

[rbuels]

what if the borders of the displayed regions were draggable, so people could expand them a little to see more context if they want?

it seems to me that would be the most intuitive way to allow people to see more context like this

[cmdcolin]

Added a dialog helper

[cmdcolin]

Regarding the suggestion of directly dragging displayed region borders, I think it might be difficult and a bit niche. I think the dialog pretty well solves it :)