Robert Buels

Separate data formatting and track configuration

1

Do away with the paradigm of formatting scripts adding configuration during formatting. Because multiple tracks can use the same data. And the default config format should be gbrowse-like.

multiple independent or linked display panes

3

When data displays get very large, independently movable and scrollable panes start to get rather necessary. Should be able to move the panes independently, or link them so that they...

REST data adapters

4

fixes #1789

Add a notification icon that displays "messages" that come from the JBrowse developers. Would download a JSON file from jbrowse.org that contains messages structured as: ```js [ { id: "unique_id",...

ability to add a custom "header bar" above the app from configuration or a plugin

9

From discussions with @childers and @mpoelchau at USDA, they have a need to be able to set custom header HTML that shows that the installation is a USDA site. A...

BAM store sequenceAdapter cannot be edited in the GUI

4

When you edit the config of a track with a BAM adapter, the sequenceAdapter slot comes up as `null` in the GUI.  @cmdcolin indicated in grooming just now that...

visualizing more complex rearrangement events

3

The breakpoint split view is a good first step, but we need more powerful tools to understand more complex rearrangement events. Figure idea: https://www.nature.com/articles/s41586-019-1913-9/figures/3 Tool that makes similar figures: http://mskilab.com/gGraph/...

sub-layout feature labels

3

add labels to each of the features in a sub-layout

assemblies from connections

5

We need to support getting assemblies from connections. For example, we should be able to point JB2 directly at a JB1 config (or maybe a whole JB1 installation) and have...

multi-track config from a CSV file or similar

2

Sometimes people have a lot of different tracks that are all the same, but just differ in their metadata and in the data file they read from. Example would be...